Differences in hyporheic-zone microbial community structure along a heavy-metal contamination gradient

Abstract

The hyporheic zone of a river is nonphotic, has steep chemical and redox gradients, and has a heterotrophic food web based on the consumption of organic carbon entrained from downwelling surface water or from upwelling groundwater. The microbial communities in the hyporheic zone are an important component of these heterotrophic food webs and perform essential functions in lotic ecosystems. Using a suite of methods (denaturing gradient gel electrophoresis, 16S rRNA phylogeny, phospholipid fatty acid analysis, direct microscopic enumeration, and quantitative PCR), we compared the microbial communities inhabiting the hyporheic zone of six different river sites that encompass a wide range of sediment metal loads resulting from large base-metal mining activity in the region. There was no correlation between sediment metal content and the total hyporheic microbial biomass present within each site. However, microbial community structure showed a significant linear relationship with the sediment metal loads. The abundances of four phylogenetic groups (groups I, II, III, and IV) most closely related to alpha-, beta-, and gamma-proteobacteria and the cyanobacteria, respectively, were determined. The sediment metal content gradient was positively correlated with group III abundance and negatively correlated with group II abundance. No correlation was apparent with regard to group I or IV abundance. This is the first documentation of a relationship between fluvially deposited heavy-metal contamination and hyporheic microbial community structure. The information presented here may be useful in predicting long-term effects of heavy-metal contamination in streams and provides a basis for further studies of metal effects on hyporheic microbial communities.

FIG. 1.

Map of field sampling sites. Each stream sampled is indicated by a square (▪). SB, Silver Bow Creek; GC, Clark Fork at Gold Creek; CF, Clark Fork at Rock Creek; LB, Little Blackfoot River; RC, Rock Creek; BH, Big Hole River.

FIG. 2.

Bar graph of CI values (mean and standard errors; n = 3) for sediments sieved from each site. Site abbreviations are as described in the legend for Fig. 1.

FIG. 3.

DGGE profiles of microbial communities inhabiting each river site. PCR products were synthesized with the universal primer pair 536fC-907r. Labels above each lane indicate which site the pattern represents. Three samples were analyzed from each site. Clostridium perfringens (C.p.) and Micrococcus luteus (M.l.) were used as reference patterns during the normalization procedure in GelCompar. Numbers and arrows indicate which bands were cut and sequenced for the phylogenetic analysis.

FIG. 4.

Phylogenetic tree of partial 16S rRNA gene sequences amplified with the 536f and 907r universal 16S primers. The symbols and represent branches that are supported by maximum likelihood, maximum parsimony, and neighbor-joining analysis with the following bootstrap values (x): •, 50% < x < 74%; ▪, x > 74%.

FIG. 5.

Abundance of bacterial groups across sites. Linear regressions of mean and standard errors (n = 3) of 16S rRNA gene copy number/gram of sediment versus CI. Each plot represents a separate qPCR response variable (i.e., groups I, II, III, and IV).

FIG. 6.

Linear regressions of community structure measures versus CI. (A) DGGE dissimilarity scores versus the difference in CI between all sites. (B) First principal component of the bacterial PLFA analysis versus the CI. Lines represent the best linear fit of the data included in the graph.