BioTechnology Institute, University of Minnesota, St. Paul, MN, USA.
J Appl Microbiol. 2013 Nov;115(5):1147-58. doi: 10.1111/jam.12323. Epub 2013 Aug 28.
A 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.
Community 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 16,400 operational taxonomic units (OTUs) were observed (4594 ± 824 OTUs per sample). Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and Verrucomicrobia accounted for 93.6 ± 1.3% of all sequence reads, and 90.5 ± 2.5% 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.
Shifts 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.
This 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.
采用基于 Illumina 的新一代测序方法，对密西西比河上游的十个地点的细菌群落进行特征描述，以评估群落的变化是否是由于上游输入和土地利用变化所致。此外，还评估了包括滤器尺寸、样品体积和样品重现性在内的方法参数，以确定群落特征描述的最佳采样方法。
使用 Illumina 新一代测序技术和 16S rDNA 的 V6 高变区来确定河流中的群落结构和多样性。共观察到 16400 个操作分类单元（OTU）（每个样本 4594 ± 824 OTU）。变形菌门、放线菌门、拟杆菌门、蓝细菌门和疣微菌门占所有序列读取的 93.6 ± 1.3%，90.5 ± 2.5%属于所有站点共有的 OTU（n = 552）。在每个站点的非共享序列读取中，33-49%与第二采样点上游潜在的人为影响有关。从原始源头开始，群落结构的多样性随着距离的增加而减少，而降雨量和 pH 值与多样性呈正相关。复制和较小的滤器孔径最小地影响群落结构的特征描述。
群落结构的变化与 OTU 的相对丰度变化有关，而不是与 OTU 的存在/不存在有关，这表明“核心细菌群落”存在于密西西比河的整个流域。
本研究是首次使用新一代测序方法对大型河流细菌群落进行特征描述的研究之一，表明上游的影响和潜在的人为影响会影响下游 OTU 的存在和相对丰度，从而导致群落结构发生显著变化。
