Bacterial community structure of acid-impacted lakes: what controls diversity?

Abstract

Although it is recognized that acidification of freshwater systems results in decreased overall species richness of plants and animals, little is known about the response of aquatic microbial communities to acidification. In this study we examined bacterioplankton community diversity and structure in 18 lakes located in the Adirondack Park (in the state of New York in the United States) that were affected to various degrees by acidic deposition and assessed correlations with 31 physical and chemical parameters. The pH of these lakes ranged from 4.9 to 7.8. These studies were conducted as a component of the Adirondack Effects Assessment Program supported by the U.S. Environmental Protection Agency. Thirty-one independent 16S rRNA gene libraries consisting of 2,135 clones were constructed from epilimnion and hypolimnion water samples. Bacterioplankton community composition was determined by sequencing and amplified ribosomal DNA restriction analysis of the clone libraries. Nineteen bacterial classes representing 95 subclasses were observed, but clone libraries were dominated by representatives of the Actinobacteria and Betaproteobacteria classes. Although the diversity and richness of bacterioplankton communities were positively correlated with pH, the overall community composition assessed by principal component analysis was not. The strongest correlations were observed between bacterioplankton communities and lake depth, hydraulic retention time, dissolved inorganic carbon, and nonlabile monomeric aluminum concentrations. While there was not an overall correlation between bacterioplankton community structure and pH, several bacterial classes, including the Alphaproteobacteria, were directly correlated with acidity. These results indicate that unlike more identifiable correlations between acidity and species richness for higher trophic levels, controls on bacterioplankton community structure are likely more complex, involving both direct and indirect processes.

FIG. 1.

Map of New York State with the Adirondack Park showing the 18 lakes sampled during this study. The locations of the 18 lakes sampled during the study are indicated (•). The inset indicates the location of New York State within the United States.

FIG. 2.

Richness estimates of 16S rRNA gene fragment clone collections from AEAP lakes and Lake George at the phylogenetic level of class (a) and subclass (b). A total of 2,135 individual clones were classified using the RDP Classifier tool (http://rdp.cme.msu.edu/classifier/classifier.jsp) from 26 samples derived from 18 different Adirondack lakes. The richness estimator Chao2 was calculated as described by Chao (4) and implemented in the EstimateS software package v7.5.1 (http://purl.oclc.org/estimates). The Chao2 richness estimator was utilized without bias correction.

FIG. 3.

Sampling sufficiency estimates of clone libraries from AEAP study lakes and Lake George. The “Large Enough” calculator (27) was used to determine whether individual clone libraries were sampled sufficiently at the class level. If the estimated phylotype richness reached an asymptote, we inferred that the library was large enough to yield a stable estimate of phylotype richness. With the exception of the libraries derived from the Big Moose Lake and Sagamore Lake epilimnion samples (b), all other samples appeared to have been sufficiently sampled.

FIG. 4.

pH versus estimated diversity (a and c) and richness (b) of bacterial community composition based on 16S rRNA gene fragment clone collections from AEAP lakes and Lake George at the phylogenetic level of class (a and b) and subclass (c). Richness was not estimated at the subclass level because sampling at this level was not sufficient. Significant correlation between diversity and pH (r = 0.387, P = 0.05) (a) and between richness and pH (r = 0.5, P = 0.01) (b) were observed. Trends at the subclass level were similar, but statistical correlations were nonsignificant (r = 0.3, P = 0.13). Diversity was estimated using the Shannon index as implemented in the BIO-DAP software (http://nhsbig.inhs.uiuc.edu). Richness for each lake sample was estimated using the Chao1 statistic as implemented using the “Large Enough” estimator (27). Richness estimates for libraries derived from the epilimnion of Big Moose Lake and Sagamore Lake were omitted because analysis suggested that these libraries were insufficiently sampled. A total of 2,135 individual clones were classified using the RDP Classifier tool (http://rdp.cme.msu.edu/classifier/classifier.jsp) from 26 samples derived from 18 Adirondack lakes. RDP classifications were assigned on 18 May 2006 (RDP update 39).

FIG. 5.

(a) Principal component analysis of bacterial community composition based on 16S rRNA gene fragment clone collections from AEAP lakes and Lake George at the phylogenetic level of class. The Actinobacteria, Betaproteobacteria, and Gammaproteobacteria accounted for significant differences (P = 0.008) between samples. A total of 75% of the variation was explained by the first two principal components (the first principal component [PC1] and the second principal component [PC2]). (b) Average distribution of the Actinobacteria, betaproteobacteria (β-proteobacteria), and gammaproteobacteria (γ-proteobacteria), and all other bacteria in each PCA-discriminated group. A total of 2,135 individual clones were classified using the RDP Classifier tool (http://rdp.cme.msu.edu/classifier/classifier.jsp) from 26 samples derived from 18 Adirondack lakes. RDP classifications were assigned on 18 May 2006 (RDP update 39).

FIG. 6.

Principal component analysis of bacterial community composition based on 16S rRNA gene fragment clone collections from AEAP lakes and Lake George at the phylogenetic level of subclass. At the phylogenetic level of subclass, most differences could be attributed to the unclassified betaproteobacteria and an unclassified Actinobacteria subclass, but differences were not significant (P > 0.05). The first two principal components (the first principal component [PC1]) and the second principal component [PC2]) explained 57% of the overall variation. The clone library from the epilimnion of Middle Settlement Lake was omitted from the analysis as an outlier. A total of 2,135 individual clones were classified using the RDP Classifier tool (http://rdp.cme.msu.edu/classifier/classifier.jsp) from 26 samples derived from 18 Adirondack lakes. RDP classifications were assigned on 18 May 2006 (RDP update 39).

FIG. 7.

Relationship between the percentage of Alphaproteobacteria and Bacteroidetes in each lake clone library and pH. The percentage of 16S rRNA gene clones in each lake sample clone library is shown. (a) Relationship between the percentage of alphaproteobacteria (α-proteobacteria) and pH (r = −0.78, P = 0.0002); (b) relationship between the percentage of Bacteroidetes and pH (r = 0.48, P = 0.02).