Bottom–up selection has an important role in microbial community assembly but is unable to account for all observed variance. Other processes like top–down selection (e.g., predation) may be partially responsible for the unexplained variance. However, top–down processes and their interaction with bottom–up selective pressures often remain unexplored. We utilised an in situ marine biofilm model system to test the effects of bottom–up (i.e., substrate properties) and top–down (i.e., large predator exclusion via 100 µm mesh) selective pressures on community assembly over time (56 days). Prokaryotic and eukaryotic community compositions were monitored using 16 S and 18 S rRNA gene amplicon sequencing. Higher compositional variance was explained by growth substrate in early successional stages, but as biofilms mature, top–down predation becomes progressively more important. Wooden substrates promoted heterotrophic growth, whereas inert substrates’ (i.e., plastic, glass, tile) lack of degradable material selected for autotrophs. Early wood communities contained more mixotrophs and heterotrophs (e.g., the total abundance of Proteobacteria and Euglenozoa was 34% and 41% greater within wood compared to inert substrates). Inert substrates instead showed twice the autotrophic abundance (e.g., cyanobacteria and ochrophyta made up 37% and 10% more of the total abundance within inert substrates than in wood). Late native (non-enclosed) communities were mostly dominated by autotrophs across all substrates, whereas high heterotrophic abundance characterised enclosed communities. Late communities were primarily under top–down control, where large predators successively pruned heterotrophs. Integrating a top–down control increased explainable variance by 7–52%, leading to increased understanding of the underlying ecological processes guiding multitrophic community assembly and successional dynamics.

自下而上的选择在微生物群落组装中具有重要作用，但无法解释所有观察到的差异。其他过程，如自上而下的选择（例如，捕食）可能是造成无法解释的差异的部分原因。然而，自上而下的过程及其与自下而上的选择压力的相互作用通常仍未得到探索。我们利用原位海洋生物膜模型系统来测试自下而上（即基质特性）和自上而下（即通过 100 µm 网格排除大型捕食者）选择压力随时间（56 天）对群落组装的影响。使用 16 S 和 18 S rRNA 基因扩增子测序监测原核和真核生物群落组成。早期演替阶段的生长底物解释了较高的成分差异，但随着生物膜的成熟，自上而下的捕食变得越来越重要。木质基质促进异养生长，而惰性基质（即塑料、玻璃、瓷砖）缺乏为自养生物选择的可降解材料。早期的木材群落含有更多的混养生物和异养生物（例如，与惰性基质相比，木材中变形菌门和裸藻门的总丰度分别高 34% 和 41%）。相反，惰性底物显示出两倍的自养丰度（例如，蓝藻和褐藻在惰性底物中的总丰度比在木材中高出 37% 和 10%）。晚期原生（非封闭）群落在所有基质中主要由自养生物主导，而高异养丰度是封闭群落的特征。晚期社区主要受自上而下的控制，大型捕食者连续修剪异养生物的地方。整合自上而下的控制将可解释的方差增加了 7-52%，从而加深了对指导多营养群落组装和演替动力学的潜在生态过程的理解。