Table_3_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.

本研究于地中海某单一离岸位置，对夏季分层水柱中15米、60米及90米深度的海水样本进行采集，并在回收后进行为期7小时的孵化实验，以探究塑料瓶封闭条件下海水微生物群落（包括丰富和稀有种类）的变化。每个深度选取两个具有代表性的样本，存储于不透明瓶中。利用‘瓶效应’研究自然微生物群落的变化，共组装获得94个宏基因组组装基因组（MAGs）和1089个宏基因组病毒连续片段，并运用宏基因组招募技术分析其丰度。检测到在整条水柱中，如Alteromonas或Erythrobacter等营养丰富的细菌呈现出显著快速生长，其生长动力学表现为‘克隆性’、‘多克隆性’或‘多物种性’，具体分类依据招募模式。此外，对光合细菌群落的生态型演替进行了显著分析，这些细菌能够在无光条件下生长于所有深度，凸显了其混合营养潜力的重大意义。此外，基于噬菌体-宿主动态研究提出的‘壁链反应’假说，揭示了病毒捕食对深层水体古菌的影响更大，证实了其在孵化过程中的显著作用。本研究在理解海洋微生物群落的动态模式和生态学机制方面取得重要进展，并强调了在采集后立即处理样本的重要性，以避免群落结构的变化。