Application of Illumina next-generation sequencing to characterize the bacterial community of the Upper Mississippi River
Application of Illumina next-generation sequencing to characterize the bacterial community of the Upper Mississippi River
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DOI：
10.1111/jam.12323
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发表时间：
2013-11-01
影响因子：
4
通讯作者：
Sadowsky, M. J.
中科院分区：
文献类型：
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作者：
Staley, C.;Unno, T.;Sadowsky, M. J.
基于illumina的下一代AimsA测序方法被用于表征密西西比河上游10个地点的细菌群落，以评估上游投入和土地利用变化可能导致的群落变化。此外，我们还评估了包括过滤器大小、样本量和样品可重复性在内的方法学参数，以确定群落表征的最佳采样方法。方法与结果采用Illumina新一代测序技术和16S rDNA的V6高变区对河流的群落结构和多样性进行了测定。共观察到16400个可操作分类单位（otu），每个样本4594824个otu。变形菌门（Proteobacteria）、放线菌门（Actinobacteria）、拟杆菌门（Bacteroidetes）、蓝藻门（Cyanobacteria）和Verrucomicrobia占所有序列reads的93613%，905 +/- 25%属于所有位点共有的OTUs （n=552）。在每个采样点的非共享序列中，33-49%与第二个采样点上游的潜在人为影响相关。α多样性随距离原始源头的远近而降低，而降雨量和pH值与α多样性呈正相关。复制和较小的过滤器孔径对群落结构的表征影响最小。结论群落结构的变化与相对丰度的变化有关，而不是与OTUs的存在与否有关，这表明整个密西西比河上游存在一个核心细菌群落。研究的意义和影响本研究是首次使用下一代测序方法表征大型河流细菌群落的研究之一，并证明上游影响和潜在的人为影响可以影响下游otu的存在和相对丰度，从而导致群落结构的显著变化。
AimsA next-generation, Illumina-based sequencing approach was used to characterize the bacterial community at ten sites along the Upper Mississippi River to evaluate shifts in the community potentially resulting from upstream inputs and land use changes. Furthermore, methodological parameters including filter size, sample volume and sample reproducibility were evaluated to determine the best sampling practices for community characterization.Methods and ResultsCommunity structure and diversity in the river was determined using Illumina next-generation sequencing technology and the V6 hypervariable region of 16S rDNA. A total of 16400 operational taxonomic units (OTUs) were observed (4594824 OTUs per sample). Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and Verrucomicrobia accounted for 93613% of all sequence reads, and 905 +/- 25% belonged to OTUs shared among all sites (n=552). Among nonshared sequence reads at each site, 33-49% were associated with potentially anthropogenic impacts upstream of the second sampling site. Alpha diversity decreased with distance from the pristine headwaters, while rainfall and pH were positively correlated with diversity. Replication and smaller filter pore sizes minimally influenced the characterization of community structure.ConclusionsShifts in community structure are related to changes in the relative abundance, rather than presence/absence of OTUs, suggesting a core bacterial community' is present throughout the Upper Mississippi River.Significance and Impact of the StudyThis study is among the first to characterize a large riverine bacterial community using a next-generation-sequencing approach and demonstrates that upstream influences and potentially anthropogenic impacts can influence the presence and relative abundance of OTUs downstream resulting in significant variation in community structure.