Premium
Application of Illumina next‐generation sequencing to characterize the bacterial community of the Upper Mississippi River
Author(s) -
Staley C.,
Unno T.,
Gould T.J.,
Jarvis B.,
Phillips J.,
Cotner J.B.,
Sadowsky M.J.
Publication year - 2013
Publication title -
journal of applied microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.889
H-Index - 156
eISSN - 1365-2672
pISSN - 1364-5072
DOI - 10.1111/jam.12323
Subject(s) - illumina dye sequencing , dna sequencing , biology , metagenomics , computational biology , genetics , gene
Aims 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. Methods and Results Community structure and diversity in the river was determined using Illumina next‐generation sequencing technology and the V6 hypervariable region of 16S r DNA . A total of 16 400 operational taxonomic units ( OTU s) were observed (4594 ± 824 OTU s per sample). P roteobacteria , A ctinobacteria, B acteroidetes , C yanobacteria and V errucomicrobia accounted for 93·6 ± 1·3% of all sequence reads, and 90·5 ± 2·5% belonged to OTU s 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. Conclusions Shifts in community structure are related to changes in the relative abundance, rather than presence/absence of OTU s, suggesting a ‘core bacterial community’ is present throughout the U pper M ississippi R iver. Significance and Impact of the Study 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 OTU s downstream resulting in significant variation in community structure.