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

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 AE 824 OTUs per sample). Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and Verrucomicrobia accounted for 93Á6 AE 1Á3% of all sequence reads, and 90Á5 AE 2Á5% 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-generationsequencing 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.

Vancomycin-Resistant Enterococci and Bacterial Community Structure following a Sewage Spill into an Aquatic Environment

“…The dominant phyla in water were consistent with those found in a study of 10 sites in the Mississippi River (Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, and Verrucomicrobia accounting for approximately 94% of sequences) (84). However, Firmicutes (containing pathogen taxa) were more prevalent in water on the days immediately after the sewage spill than at later dates compared to the consistent low levels in the Mississippi River samples.…”

Regional Similarities and Consistent Patterns of Local Variation in Beach Sand Bacterial Communities throughout the Northern Hemisphere

“…One of the key findings of this study is the high degree of regional taxonomic and, in some cases, phylogenetic similarity. This may be driven in part by interactions between the sand and water communities, since persistent core microbiomes for both freshwater and marine environments have been previously suggested (53,54). We further show the presence of highly similar local community dynamics within the same beach, where moisture, most likely resulting from tidal cycles, is a major driver of the bacterial communities present.…”

The Bacterial Communities of Full-Scale Biologically Active, Granular Activated Carbon Filters Are Stable and Diverse and Potentially Contain Novel Ammonia-Oxidizing Microorganisms

“…Triplicate PCRs targeting the V6 region of the 16S rRNA were performed on each DNA extract as described previously (17). Briefly, the PCR primers were a mixture of five modified 967F primers known to amplify both Bacteria and Archaea (18) coupled to the 1046R primer with a six-base multiplexing identification barcode attached to the 5= end (19).…”