Abstract
Taxonomic characterization of environmental microbial communities via high-throughput DNA sequencing has revealed that patterns in microbial biogeography affect community structure. However, shifts in functional diversity related to variation in taxonomic composition are poorly understood. To overcome limitations due to the prohibitive cost of high-depth metagenomic sequencing, tools to infer functional diversity based on phylogenetic distributions of functional traits have been developed. In this study we characterized functional microbial diversity at 11 sites along the Mississippi River in Minnesota using both metagenomic sequencing and functional-inference-based (PICRUSt) approaches. This allowed us to determine how distance and variation in land cover throughout the river influenced the distribution of functional traits, as well as to validate PICRUSt inferences. The distribution and abundance of functional traits, by metagenomic analysis, were similar among sites, with a median standard deviation of 0.0002% among tier 3 functions in KEGG. Overall inferred functional variation was significantly different (P ≤ 0.035) between two water basins surrounded by agricultural vs. developed land cover, and abundances of bacterial orders that correlated with functional traits by metagenomic analysis were greater where abundances of the trait were inferred to be higher. PICRUSt inferences were significantly correlated (r = 0.147, P = 1.80 × 10−30) with metagenomic annotations. Discrepancies between metagenomic and PICRUSt taxonomic-functional relationships, however, suggested potential functional redundancy among abundant and rare taxa that impeded the ability to accurately assess unique functional traits among rare taxa at this sequencing depth. Results of this study suggest that a suite of “core functional traits” is conserved throughout the river and distributions of functional traits, rather than specific taxa, may shift in response to environmental heterogeneity.
Highlights
Over the last 30 years, sequencing of the 16S rRNA gene has allowed for expansive characterization of microbial biodiversity from a variety of hosts and habitats (Olsen et al, 1986)
TAXONOMIC CHARACTERIZATION OF BACTERIAL COMMUNITIES Bacterial communities characterized by both shotgun metagenomic analyses and 16S rDNA were similar and were dominated primarily by Burkholderiales and Actinobacteria (Figure 2)
Non-bacterial orders, consisting primarily of orders belonging to the kingdoms Plantae and Protista and the phylum Arthropoda, were identified in the metagenomic data, but these were present at very low abundances (
Summary
Over the last 30 years, sequencing of the 16S rRNA gene has allowed for expansive characterization of microbial biodiversity from a variety of hosts and habitats (Olsen et al, 1986). The emergence of next-generation sequencing technologies has supported the predominance of these groups in freshwater riverine ecosystems, and has allowed for assessments of variability among bacterial communities (Ghai et al, 2011; Portillo et al, 2012; Staley et al, 2013) These studies have demonstrated that the taxonomic bacterial community structure in aquatic environments is, at least in part, shaped by gradients of physicochemical and biotic parameters (Gilbert et al, 2009; Fortunato and Crump, 2011; Fortunato et al, 2012; Portillo et al, 2012). These include: (1) “to what extent does a core microbial community exist?” and (2) “to what extent is variation in taxonomic community composition meaningful?”
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