Table_4_Prokaryotic Population Dynamics and Viral Predation in a Marine Succession Experiment Using Metagenomics.XLSX

We performed an incubation experiment of seawater confined in plastic bottles with samples collected at three depths (15, 60, and 90 m) after retrieval from a single offshore location in the Mediterranean Sea, from a late summer stratified water column. Two samples representative of each depth were collected and stored in opaque bottles after two periods of 7 h. We took advantage of the “bottle effect” to investigate changes in the natural microbial communities (abundant and rare). We recovered 94 metagenome-assembled genomes (MAGs) and 1089 metagenomic viral contigs and examined their abundance using metagenomic recruitment. We detected a significant fast growth of copiotrophic bacteria such as Alteromonas or Erythrobacter throughout the entire water column with different dynamics that we assign to “clonal,” “polyclonal,” or “multispecies” depending on the recruitment pattern. Results also showed a marked ecotype succession in the phototropic picocyanobacteria that were able to grow at all the depths in the absence of light, highlighting the importance of their mixotrophic potential. In addition, “wall-chain-reaction” hypothesis based on the study of phage–host dynamics showed the higher impact of viral predation on archaea in deeper waters, evidencing their prominent role during incubations. Our results provide a step forward in understanding the mechanisms underlying dynamic patterns and ecology of the marine microbiome and the importance of processing the samples immediately after collection to avoid changes in the community structure.

本研究针对地中海海域单一离岸位置在不同深度（15米、60米和90米）采集的海水样本进行了塑料瓶封闭培养实验，样本采集自晚夏期的分层水柱。在每个深度收集了两个具有代表性的样本，并在两次7小时的培养周期后将其存放在不透明瓶中。利用‘瓶效应’研究自然微生物群落（丰富和稀有）的变化。我们恢复了94个宏基因组组装基因（MAGs）和1089个宏基因组病毒连续片段，并使用宏基因组招募技术对其丰度进行了分析。我们发现，如Alteromonas或Erythrobacter等营养丰富的细菌在整个水柱中呈现出显著的生长加速，其动态变化依据招募模式被划分为‘克隆性’、‘多克隆性’或‘多物种性’。研究结果显示，能够在无光条件下生长的光合型小型蓝藻也出现了明显的生态型更替，凸显了其混合营养潜力的意义。此外，基于噬菌体-宿主动态研究提出的‘壁链反应’假说表明，在深层水中病毒捕食对古菌的影响更大，证实了它们在培养过程中的突出作用。我们的研究结果在理解海洋微生物群落的动态模式和生态学以及样本采集后立即处理以避免群落结构变化的重要性方面迈出了重要一步。