Environmental Bacteria Targeted Locus (Loci)

The vastness of microbial diversity implies that an almost infinite number of individuals needs to be identified to accurately describe such communities. Practical and economical constraints may therefore prevent appropriate study designs. However, for many questions in ecology it is not essential to know the actual diversity but rather the trends among samples thereof. It is, hence, important to know to what depth microbial communities need to be sampled to accurately measure trends in diversity. We used three data-sets of freshwater and sediment bacteria, where diversity was explored using 454 pyrosequencing. Each data-set contained 6-15 communities from which 15000-20000 16S rRNA gene sequences each were obtained. These data-sets were subsampled repeatedly to ten different depths down to 200 sequences per community. Diversity estimates varied with sequencing depth, yet, trends in diversity among samples were less sensitive. We found that 1000 denoised sequences per sample explained to 90%% the trends in beta-diversity (Bray-Curtis index) among samples observed for 15000-20000 sequences. Similarly, 5000 denoised sequences were sufficient to describe trends in alpha-diversity (Shannon index) with the same accuracy. Further, 5000 denoised sequences captured to more than 80%% the trends in Chao1 richness and Pielou’s evenness. Lake water and sediment bacteria were collected from mesotrophic streams and oligotrophic and mesotrophic lakes in Sweden.

微生物多样性的广度意味着，若要精准刻画这类群落，几乎需要对无限多的个体进行物种鉴定。因此，实际操作与经济层面的限制往往会阻碍合理的研究方案设计。然而，对于生态学中的诸多研究问题而言，并非必须知晓真实的多样性水平，而是需要了解样本间的多样性变化趋势。因此，明确为精准测定多样性变化趋势所需的微生物群落测序深度，便成为一项关键课题。本研究使用了三组淡水与沉积物细菌数据集，均通过454焦磷酸测序（454 pyrosequencing）探究其多样性。每组数据集包含6至15个细菌群落，每个群落均可获取15000至20000条16S rRNA基因序列。研究人员对这些数据集进行多次亚采样，设置了从每个群落200条序列起的10种不同测序深度梯度。多样性估计值会随测序深度发生变化，但样本间的多样性变化趋势受测序深度的影响相对较小。研究发现，当每个样本使用1000条去噪序列时，可解释90%的、基于15000至20000条序列观测到的样本间β多样性（beta-diversity，Bray-Curtis指数）变化趋势。类似地，若要以同等精度刻画α多样性（alpha-diversity，香农指数）的变化趋势，5000条去噪序列便已足够。此外，5000条去噪序列可覆盖超过80%的Chao1丰富度与皮尔洛均匀度（Pielou's evenness）的变化趋势。本研究中的湖水与沉积物细菌样本采集自瑞典的中营养溪流以及寡营养与中营养湖泊。