Spatial and temporal processes shaping microbial communities are inseparably linked but rarely studied together. By Illumina 16S rRNA sequencing, we monitored soil bacteria in 360 stations on a 100 square meter plot distributed across six intra-annual samplings in a rarely managed, temperate grassland. Using a multi-tiered approach, we tested the extent to which stochastic or deterministic processes influenced the composition of local communities. A combination of phylogenetic turnover analysis and null modeling demonstrated that either homogenization by unlimited stochastic dispersal or scenarios, in which neither stochastic processes nor deterministic forces dominated, explained local assembly processes. Thus, the majority of all sampled communities (82%) was rather homogeneous with no significant changes in abundance-weighted composition. However, we detected strong and uniform taxonomic shifts within just nine samples in early summer. Thus, community snapshots sampled from single points in time or space do not necessarily reflect a representative community state. The potential for change despite the overall homogeneity was further demonstrated when the focus shifted to the rare biosphere. Rare OTU turnover, rather than nestedness, characterized abundance-independent β-diversity. Accordingly, boosted generalized additive models encompassing spatial, temporal and environmental variables revealed strong and highly diverse effects of space on OTU abundance, even within the same genus. This pure spatial effect increased with decreasing OTU abundance and frequency, whereas soil moisture – the most important environmental variable – had an opposite effect by impacting abundant OTUs more than the rare ones. These results indicate that – despite considerable oscillation in space and time – the abundant and resident OTUs provide a community backbone that supports much higher β-diversity of a dynamic rare biosphere. Our findings reveal complex interactions among space, time, and environmental filters within bacterial communities in a long-established temperate grassland.

形成微生物群落的时空过程密不可分，但很少一起研究。通过Illumina 16S rRNA测序，我们在一个很少管理的温带草原上的六个年度年度采样中分布的一个100平方米的样地中的360个站点中监测了土壤细菌。使用多层方法，我们测试了随机或确定性过程对当地社区构成的影响程度。系统发育周转分析和无效模型的结合表明，通过无限制的随机分散进行均质化或在随机过程和确定性力都不占主导的情况下进行局部组装过程的解释。因此，所有抽样社区中的大多数（82％）都相当均质，丰度加权组成没有明显变化。但是，我们在初夏的九个样本中检测到了强烈而统一的分类学变化。因此，从单个时间或空间点采样的社区快照不一定反映代表性的社区状态。当重点转移到稀有生物圈时，尽管总体上具有同质性，但改变的潜力得到了进一步证明。很少的OTU周转率，而不是嵌套度，其特征是不依赖丰度的β多样性。因此，增强的包含空间，时间和环境变量的广义加性模型揭示了即使在同一属中，空间对OTU丰度的强烈且高度不同的影响。这种纯净的空间效应随着OTU丰度和频率的降低而增加，而土壤水分（最重要的环境变量）的影响则相反，其对丰富的OTU的影响要大于对稀有OTU的影响。这些结果表明，尽管时空发生了相当大的波动，但大量的常驻OTU提供了一个社区主干，可支持动态稀有生物圈的更高的β多样性。我们的发现揭示了在一个古老的温带草原细菌群落中，空间，时间和环境过滤器之间的复杂相互作用。