Sediment enzyme activities and microbial community diversity in an oligotrophic drinking water reservoir, eastern China

Abstract

Drinking water reservoir plays a vital role in the security of urban water supply, yet little is known about microbial community diversity harbored in the sediment of this oligotrophic freshwater environmental ecosystem. In the present study, integrating community level physiological profiles (CLPPs), nested polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and clone sequence technologies, we examined the sediment urease and protease activities, bacterial community functional diversity, genetic diversity of bacterial and fungal communities in sediments from six sampling sites of Zhou cun drinking water reservoir, eastern China. The results showed that sediment urease activity was markedly distinct along the sites, ranged from 2.48 to 11.81 mg NH₃-N/(g·24 h). The highest average well color development (AWCD) was found in site C, indicating the highest metabolic activity of heterotrophic bacterial community. Principal component analysis (PCA) revealed tremendous differences in the functional (metabolic) diversity patterns of the sediment bacterial communities from different sites. Meanwhile, DGGE fingerprints also indicated spatial changes of genetic diversity of sediment bacterial and fungal communities. The sequence BLAST analysis of all the sediment samples found that Comamonas sp. was the dominant bacterial species harbored in site A. Alternaria alternate, Allomyces macrogynus and Rhizophydium sp. were most commonly detected fungal species in sediments of the Zhou cun drinking water reservoir. The results from this work provide new insights about the heterogeneity of sediment microbial community metabolic activity and genetic diversity in the oligotrophic drinking water reservoir.

Figure 1. Kinetics of average well color development (AWCD _590nm) curve of sediment bacterial communities.

Sediments were collected from each six sampling sites (site A, site B, site C, site D, site E, site F). The data shown are the means and standard error (S.E) (n=3).

Figure 2. Functional diversity index of sediment bacterial community.

(A) AWCD _(590nm), (B) Species richness (R) and (C) Shannon’s diversity (H) of bacterial community in the sediments from each six sampling sites (site A, site B, site C, site D, site E, site F) in the Zhou cun drinking water reservoir, eastern China. Bars followed by the same capital letter indicate no significant difference by Tukey-Kramer HSD (P<0.05). The data shown are the means and standard error (S.E) (n=3).

Figure 3. Principle component analyses (PCA) of bacterial functional diversity.

Sediments were collected from each six sampling sites (site A, site B, site C, site D, site E, site F) in the Zhou cun drinking water reservoir, eastern China. Data were calculated based on sole carbon substrate utilization pattern using BIOLOG ECO micro plates after incubation of 144 h. Numbers in brackets represent the percentage of variation explained by each factor, PC1 explains 13.80% of the variance of the data and PC2 explains 12.12% of the variance in the data, respectively. Bars represent plus one standard error (S.E) (n=3).

Figure 4. DGGE profiles of PCR-amplified 16S rRNA gene (V3 region).

(A) Fragments in a denaturing from 30% to 70% gradient gel. B1-B8 represents sequenced bands in the bacterial community DGGE gel. (B) Redundancy Analysis (RDA) of bacterial community in the sediments from each six sampling sites (site A, site B, site C, site D, site E, site F) in the Zhou cun drinking water reservoir, eastern China. Samples are represented by open circles and the capital letters refer to the sampling sites. Numbers in brackets represent the percentage of variation explained by each factor, RDA1 explains 63.26% of the variance of the data and RDA2 explains 22.35% of the variance in the data, respectively. Significant factors for variation extracted from environmental data (sediment urease and protease activity) are given as vectors.

Figure 5. DGGE profiles of PCR-amplified 18S rRNA gene-internal transcribed spacer.

(A) Fragments in a denaturing from 30% to 70% gradient gel. F1-F6 represents sequenced bands in the fungal community DGGE gel. (B)Redundancy Analysis (RDA) of fungal community in the sediments from each six sampling sites (site A, site B, site C, site D, site E, site F) in the Zhou cun drinking water reservoir, eastern China. Samples are represented by open circles and capital letters refer to the sampling sites. Numbers in brackets represent the percentage of variation explained by each factor, RDA1 explains 35.40% of the variance of the data and RDA2 explains 16.00% of the variance in the data, respectively. Significant factors for variation extracted from environmental data (sediment urease and protease activity) are given as vectors.

Figure 6. Phylogenetic affiliation of sequences retrieved from sediment (A) bacterial community and (B) fungal community.

Bootstrap values (>50%) are indicated at nodes (1000 replications). Sequences obtained in the present study were shown in boldface. The internal letter and number (e.g. B1, F1) represents sequences in the DGGE fingerprints band B1 and F1. Scale bar represents 0.5 substitutions per nucleotide position.