Format

Send to

Choose Destination
See comment in PubMed Commons below
J Appl Microbiol. 2013 Nov;115(5):1147-58. doi: 10.1111/jam.12323. Epub 2013 Aug 28.

Application of Illumina next-generation sequencing to characterize the bacterial community of the Upper Mississippi River.

Author information

1
BioTechnology Institute, University of Minnesota, St. Paul, MN, USA.

Abstract

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 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.

CONCLUSIONS:

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.

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 OTUs downstream resulting in significant variation in community structure.

KEYWORDS:

environmental/recreational water; genomics; microbial diversity; microbial structure; water quality

PMID:
23924231
DOI:
10.1111/jam.12323
[Indexed for MEDLINE]
Free full text
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Wiley
    Loading ...
    Support Center