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, 60 (4), 784-95

Characterization of Archaeal Community in Contaminated and Uncontaminated Surface Stream Sediments

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Characterization of Archaeal Community in Contaminated and Uncontaminated Surface Stream Sediments

Iris Porat et al. Microb Ecol.

Abstract

Archaeal communities from mercury and uranium-contaminated freshwater stream sediments were characterized and compared to archaeal communities present in an uncontaminated stream located in the vicinity of Oak Ridge, TN, USA. The distribution of the Archaea was determined by pyrosequencing analysis of the V4 region of 16S rRNA amplified from 12 streambed surface sediments. Crenarchaeota comprised 76% of the 1,670 archaeal sequences and the remaining 24% were from Euryarchaeota. Phylogenetic analysis further classified the Crenarchaeota as a Freshwater Group, Miscellaneous Crenarchaeota group, Group I3, Rice Cluster VI and IV, Marine Group I and Marine Benthic Group B; and the Euryarchaeota into Methanomicrobiales, Methanosarcinales, Methanobacteriales, Rice Cluster III, Marine Benthic Group D, Deep Sea Hydrothermal Vent Euryarchaeota 1 and Eury 5. All groups were previously described. Both hydrogen- and acetate-dependent methanogens were found in all samples. Most of the groups (with 60% of the sequences) described in this study were not similar to any cultivated isolates, making it difficult to discern their function in the freshwater microbial community. A significant decrease in the number of sequences, as well as in the diversity of archaeal communities was found in the contaminated sites. The Marine Group I, including the ammonia oxidizer Nitrosopumilus maritimus, was the dominant group in both mercury and uranium/nitrate-contaminated sites. The uranium-contaminated site also contained a high concentration of nitrate, thus Marine Group I may play a role in nitrogen cycle.

Figures

Figure 1
Figure 1
Sampling locations in creeks near Oak Ridge, TN, USA. The location of DOE Y-12 National Security Complex (Y-12 NSC) and the sampling sites are indicated. The location coordinates for sampling sites are: Hinds Creek (HC) 36°08′N, 84°03′W; White Oak Creek (WC) 35°55′N, 84°18′W; Bear Creek (BC) 35°58′N, 84°16′W; East Fork Poplar Creek K23.4 (EF23): 35°59′N, 84°14′W; East Fork Poplar Creek K13.8 (EF13) 35°59′N, 84°18′W; East Fork Poplar Creek K6.3 (EF6) 35°57′N, 84°21′W
Figure 2
Figure 2
Redundancy analysis (RDA) of the archaeal sequences in correlation with chemical parameters. A total of 71 clusters at 95% sequence identity were used for analysis. RDA with clusters obtained grouped at 97% sequence identity showed similar distribution (not shown). Open symbols represent samples taken in mid-channel and closed symbols represent samples taken near the bank of stream. Correlations with SO42− and temperature are indicated. The regression scores (R) for SO42− is 0.4312 for axis 1 and −0.9024 for axis 2. The R scores for temperature are −0.9082 for axis 1 and −0.4185 for axis 2. In addition, pH showed positive correlation with SO42−. Crenarchaeota clusters are indicated in bold and Euryarchaeota clusters are indicated in italic
Figure 3
Figure 3
Neighbor-joining phylogenetic trees of crenarchaeotal (a) and euryarchaeotal (b) V4 region of 16S rRNA gene sequences obtained from all samples. Similar topology for both phylogenetic trees was obtained when only full length sequences of published 16S rRNA genes were included into analysis (not shown). Bootstrap values greater than 50% are indicated at the nodes. The scale bar indicates 0.05 nucleotide substitution per sequence position. Clusters obtained during this study are indicated in bold; the number of sequences in the corresponding cluster followed by the number of samples these sequences were found in (a total of 12 samples) is given in parentheses. Clusters represent a group of sequences with 95% identity. The complete list of sequences in each cluster is given in Supplemental Table 2. Accession numbers of published sequences are indicated in square brackets. Previously described major phylogenetic lineages are indicated. The sequences of Methanosarcina acetivorans C2A [AE010299] and Thermococcus kodakarensis NR [028216] serve as an out-group in A and Nitrosopumilus maritimus SCM1 [CP000866] and Thermoproteus neutrophilus [AB009618] were used for an out-group in B
Figure 3
Figure 3
Neighbor-joining phylogenetic trees of crenarchaeotal (a) and euryarchaeotal (b) V4 region of 16S rRNA gene sequences obtained from all samples. Similar topology for both phylogenetic trees was obtained when only full length sequences of published 16S rRNA genes were included into analysis (not shown). Bootstrap values greater than 50% are indicated at the nodes. The scale bar indicates 0.05 nucleotide substitution per sequence position. Clusters obtained during this study are indicated in bold; the number of sequences in the corresponding cluster followed by the number of samples these sequences were found in (a total of 12 samples) is given in parentheses. Clusters represent a group of sequences with 95% identity. The complete list of sequences in each cluster is given in Supplemental Table 2. Accession numbers of published sequences are indicated in square brackets. Previously described major phylogenetic lineages are indicated. The sequences of Methanosarcina acetivorans C2A [AE010299] and Thermococcus kodakarensis NR [028216] serve as an out-group in A and Nitrosopumilus maritimus SCM1 [CP000866] and Thermoproteus neutrophilus [AB009618] were used for an out-group in B
Figure 4
Figure 4
Archaeal community structures within each sampling site. The sequences from samples collected at mid-channel and stream bank were combined for each location. The sequences were grouped by major phylogenetic lineages presented in Fig. 3. Only groups with more than five sequences were included. For the larger groups, the number of sequences is indicated. a Crenarchaeota community; b Euryarchaeota community

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