Limits...
Core functional traits of bacterial communities in the Upper Mississippi River show limited variation in response to land cover.

Staley C, Gould TJ, Wang P, Phillips J, Cotner JB, Sadowsky MJ - Front Microbiol (2014)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: BioTechnology Institute, University of Minnesota St. Paul, MN, USA.

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.

No MeSH data available.


Relative location of sampling sites along the Mississippi River and major contributing rivers.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4126211&req=5

Figure 1: Relative location of sampling sites along the Mississippi River and major contributing rivers.

Mentions: Samples were collected from May through July in 2012 from 11 sites along the Mississippi River and major contributing rivers beginning at the headwaters at Lake Itasca to the southern border of Minnesota, near La Crescent. The relative locations of sampling sites are shown in Figure 1, and exact sampling locations were previously described (Staley et al., 2013). Briefly, bacteria were concentrated from 40 L water samples on 0.45-μm-pore-size filters and elutriated by vortexing in pyrophosphate buffer, as described previously (Staley et al., 2013). We have previously compared the effect of filter pore size on the bacterial community characterized and found that this pore size allows for efficient filtration of large volumes of water used here (Staley et al., 2013), with minimal influence on overall estimates of community composition. A total of six cell pellets per site representing approximately 6–7 L of water each, were stored at −80°C until used. These pellets were used for a variety of experiments, not all of which are described here. DNA was extracted from cell pellets from each site (n = 11), 16S rDNA amplification, and sequencing were performed and reported in detail elsewhere (Staley et al., 2013), using the Metagenomic DNA Isolation Kit for Water (Epicentre, Madison, WI) and the 967F/1046R barcoded primer set (Sogin et al., 2006).


Core functional traits of bacterial communities in the Upper Mississippi River show limited variation in response to land cover.

Staley C, Gould TJ, Wang P, Phillips J, Cotner JB, Sadowsky MJ - Front Microbiol (2014)

Relative location of sampling sites along the Mississippi River and major contributing rivers.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4126211&req=5

Figure 1: Relative location of sampling sites along the Mississippi River and major contributing rivers.
Mentions: Samples were collected from May through July in 2012 from 11 sites along the Mississippi River and major contributing rivers beginning at the headwaters at Lake Itasca to the southern border of Minnesota, near La Crescent. The relative locations of sampling sites are shown in Figure 1, and exact sampling locations were previously described (Staley et al., 2013). Briefly, bacteria were concentrated from 40 L water samples on 0.45-μm-pore-size filters and elutriated by vortexing in pyrophosphate buffer, as described previously (Staley et al., 2013). We have previously compared the effect of filter pore size on the bacterial community characterized and found that this pore size allows for efficient filtration of large volumes of water used here (Staley et al., 2013), with minimal influence on overall estimates of community composition. A total of six cell pellets per site representing approximately 6–7 L of water each, were stored at −80°C until used. These pellets were used for a variety of experiments, not all of which are described here. DNA was extracted from cell pellets from each site (n = 11), 16S rDNA amplification, and sequencing were performed and reported in detail elsewhere (Staley et al., 2013), using the Metagenomic DNA Isolation Kit for Water (Epicentre, Madison, WI) and the 967F/1046R barcoded primer set (Sogin et al., 2006).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: BioTechnology Institute, University of Minnesota St. Paul, MN, USA.

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.

No MeSH data available.