Nemergut Diana R, Knelman Joseph E, Ferrenberg Scott, Bilinski Teresa, Melbourne Brett, Jiang Lin, Violle Cyrille, Darcy John L, Prest Tiffany, Schmidt Steven K, Townsend Alan R
Department of Biology, Duke University, Durham, NC, USA.
Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO, USA.
ISME J. 2016 May;10(5):1147-56. doi: 10.1038/ismej.2015.191. Epub 2015 Nov 13.
Trait-based studies can help clarify the mechanisms driving patterns of microbial community assembly and coexistence. Here, we use a trait-based approach to explore the importance of rRNA operon copy number in microbial succession, building on prior evidence that organisms with higher copy numbers respond more rapidly to nutrient inputs. We set flasks of heterotrophic media into the environment and examined bacterial community assembly at seven time points. Communities were arrayed along a geographic gradient to introduce stochasticity via dispersal processes and were analyzed using 16 S rRNA gene pyrosequencing, and rRNA operon copy number was modeled using ancestral trait reconstruction. We found that taxonomic composition was similar between communities at the beginning of the experiment and then diverged through time; as well, phylogenetic clustering within communities decreased over time. The average rRNA operon copy number decreased over the experiment, and variance in rRNA operon copy number was lowest both early and late in succession. We then analyzed bacterial community data from other soil and sediment primary and secondary successional sequences from three markedly different ecosystem types. Our results demonstrate that decreases in average copy number are a consistent feature of communities across various drivers of ecological succession. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, ranging from cells to populations and communities, with implications for both microbial ecology and evolution.
基于特征的研究有助于阐明驱动微生物群落组装和共存模式的机制。在此，我们基于先前的证据，即具有较高拷贝数的生物体对养分输入的反应更快，采用基于特征的方法来探究rRNA操纵子拷贝数在微生物演替中的重要性。我们将异养培养基烧瓶置于环境中，并在七个时间点检查细菌群落的组装情况。群落沿着地理梯度排列，通过扩散过程引入随机性，并使用16S rRNA基因焦磷酸测序进行分析，rRNA操纵子拷贝数则使用祖先特征重建进行建模。我们发现，在实验开始时，群落之间的分类组成相似，然后随时间发生分化；此外，群落内的系统发育聚类随时间减少。在整个实验过程中，rRNA操纵子的平均拷贝数下降，rRNA操纵子拷贝数的方差在演替早期和晚期均最低。然后，我们分析了来自三种截然不同生态系统类型的其他土壤和沉积物原生和次生演替序列中的细菌群落数据。我们的结果表明，平均拷贝数的下降是不同生态演替驱动因素下群落的一个一致特征。重要的是，我们的工作支持了拷贝数特征在从细胞到种群和群落的多个生物组织层次上的扩展，这对微生物生态学和进化都具有重要意义。
