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Comparisons of the composition and biogeographic distribution of the bacterial communities occupying South African thermal springs with those inhabiting deep subsurface fracture water.

Magnabosco C, Tekere M, Lau MC, Linage B, Kuloyo O, Erasmus M, Cason E, van Heerden E, Borgonie G, Kieft TL, Olivier J, Onstott TC - Front Microbiol (2014)

Bottom Line: Proteobacteria were identified as the dominant phylum within both subsurface and thermal spring environments, but only one genera, Rheinheimera, was identified among all samples.Using Morisita similarity indices as a metric for pairwise comparisons between sites, we found that the communities of thermal springs are highly distinct from subsurface datasets.Although the Limpopo thermal springs do not appear to provide a new window for viewing subsurface bacterial communities, we report that the taxonomic compositions of the subsurface sites studied are more similar than previous results would indicate and provide evidence that the microbial communities sampled at depth are more correlated to subsurface conditions than geographical distance.

View Article: PubMed Central - PubMed

Affiliation: Department of Geosciences, Princeton University Princeton, NJ, USA.

ABSTRACT
South Africa has numerous thermal springs that represent topographically driven meteoric water migrating along major fracture zones. The temperature (40-70°C) and pH (8-9) of the thermal springs in the Limpopo Province are very similar to those of the low salinity fracture water encountered in the South African mines at depths ranging from 1.0 to 3.1 km. The major cation and anion composition of these thermal springs are very similar to that of the deep fracture water with the exception of the dissolved inorganic carbon and dissolved O2, both of which are typically higher in the springs than in the deep fracture water. The in situ biological relatedness of such thermal springs and the subsurface fracture fluids that feed them has not previously been evaluated. In this study, we evaluated the microbial diversity of six thermal spring and six subsurface sites in South Africa using high-throughput sequencing of 16S rRNA gene hypervariable regions. Proteobacteria were identified as the dominant phylum within both subsurface and thermal spring environments, but only one genera, Rheinheimera, was identified among all samples. Using Morisita similarity indices as a metric for pairwise comparisons between sites, we found that the communities of thermal springs are highly distinct from subsurface datasets. Although the Limpopo thermal springs do not appear to provide a new window for viewing subsurface bacterial communities, we report that the taxonomic compositions of the subsurface sites studied are more similar than previous results would indicate and provide evidence that the microbial communities sampled at depth are more correlated to subsurface conditions than geographical distance.

No MeSH data available.


Related in: MedlinePlus

Oligotypes of abundant genera. Entropy profiles for Desulforudis(Ai), Dehalogenimonas(B), and Dehalogenimonas OTU1 (Ci) are a discrete xy plot where the x-axis is the nucleotide position in the alignment and the y-axis is the calculated Shannon entropy for that position. Figures (Aii) and (Cii) display the relative abundance of the oligotypes observed. For Desulforudis, only one oligotype (AA) was observed while Dehalogenimonas revealed two oligotypes (AA, GG). The position of these distinctive nucleotides can be found in the entropy plot of (Ci). The elevated entropy at positions 1 and 40 reveal that these positions are where the single nucleotide changes occur.
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Figure 4: Oligotypes of abundant genera. Entropy profiles for Desulforudis(Ai), Dehalogenimonas(B), and Dehalogenimonas OTU1 (Ci) are a discrete xy plot where the x-axis is the nucleotide position in the alignment and the y-axis is the calculated Shannon entropy for that position. Figures (Aii) and (Cii) display the relative abundance of the oligotypes observed. For Desulforudis, only one oligotype (AA) was observed while Dehalogenimonas revealed two oligotypes (AA, GG). The position of these distinctive nucleotides can be found in the entropy plot of (Ci). The elevated entropy at positions 1 and 40 reveal that these positions are where the single nucleotide changes occur.

Mentions: Oligotyping was performed on all subsurface sequences related to the two most abundant subsurface genera, Ca. Desulforudis and Dehalogenimonas, to identify nucleotide level variation within the OTU and genus level. A total of 1,381 sequences were identified as related to Ca. Desulforudis while 1,226 sequences were identified as related to Dehalogenimonas representing 62 and 164 OTUs at the 97% identity level, respectively. Entropy profiles for all sequences from each genus can be found in Figures 4Ai,B. Eren et al. (2013a) reported that random sequencing errors generate entropy values near or below 0.2. For Ca. Desulforudis, 59 of the 61 positions exhibited Shannon entropy values less than 0.2, while the remaining two positions had entropy values of 0.2487 and 0.2125. Oligotyping of these 2 positions (−c 2, −M 20) revealed that only one oligotype was present (Figure 4Aii), suggesting that the Ca. Desulforudis genus identified within the subsurface contain highly similar V6 regions. On the other hand, the Shannon entropy profile of all sequences related to Dehalogenimonas showed that 33 of the 61 positions of the V6 region contained entropy values greater than 0.2 (Figure 4B). Due to the large number of high entropy positions in Dehalogenimonas-related V6 sequences, oligotyping was performed on the most abundant OTU0.03 (n = 260) instead of the complete set of sequences assigned to this genus. For this OTU, Shannon entropy profiles indicated two high entropy positions that decomposed into 2 oligotypes (−c 2, −M 20; Figure 4C).


Comparisons of the composition and biogeographic distribution of the bacterial communities occupying South African thermal springs with those inhabiting deep subsurface fracture water.

Magnabosco C, Tekere M, Lau MC, Linage B, Kuloyo O, Erasmus M, Cason E, van Heerden E, Borgonie G, Kieft TL, Olivier J, Onstott TC - Front Microbiol (2014)

Oligotypes of abundant genera. Entropy profiles for Desulforudis(Ai), Dehalogenimonas(B), and Dehalogenimonas OTU1 (Ci) are a discrete xy plot where the x-axis is the nucleotide position in the alignment and the y-axis is the calculated Shannon entropy for that position. Figures (Aii) and (Cii) display the relative abundance of the oligotypes observed. For Desulforudis, only one oligotype (AA) was observed while Dehalogenimonas revealed two oligotypes (AA, GG). The position of these distinctive nucleotides can be found in the entropy plot of (Ci). The elevated entropy at positions 1 and 40 reveal that these positions are where the single nucleotide changes occur.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4269199&req=5

Figure 4: Oligotypes of abundant genera. Entropy profiles for Desulforudis(Ai), Dehalogenimonas(B), and Dehalogenimonas OTU1 (Ci) are a discrete xy plot where the x-axis is the nucleotide position in the alignment and the y-axis is the calculated Shannon entropy for that position. Figures (Aii) and (Cii) display the relative abundance of the oligotypes observed. For Desulforudis, only one oligotype (AA) was observed while Dehalogenimonas revealed two oligotypes (AA, GG). The position of these distinctive nucleotides can be found in the entropy plot of (Ci). The elevated entropy at positions 1 and 40 reveal that these positions are where the single nucleotide changes occur.
Mentions: Oligotyping was performed on all subsurface sequences related to the two most abundant subsurface genera, Ca. Desulforudis and Dehalogenimonas, to identify nucleotide level variation within the OTU and genus level. A total of 1,381 sequences were identified as related to Ca. Desulforudis while 1,226 sequences were identified as related to Dehalogenimonas representing 62 and 164 OTUs at the 97% identity level, respectively. Entropy profiles for all sequences from each genus can be found in Figures 4Ai,B. Eren et al. (2013a) reported that random sequencing errors generate entropy values near or below 0.2. For Ca. Desulforudis, 59 of the 61 positions exhibited Shannon entropy values less than 0.2, while the remaining two positions had entropy values of 0.2487 and 0.2125. Oligotyping of these 2 positions (−c 2, −M 20) revealed that only one oligotype was present (Figure 4Aii), suggesting that the Ca. Desulforudis genus identified within the subsurface contain highly similar V6 regions. On the other hand, the Shannon entropy profile of all sequences related to Dehalogenimonas showed that 33 of the 61 positions of the V6 region contained entropy values greater than 0.2 (Figure 4B). Due to the large number of high entropy positions in Dehalogenimonas-related V6 sequences, oligotyping was performed on the most abundant OTU0.03 (n = 260) instead of the complete set of sequences assigned to this genus. For this OTU, Shannon entropy profiles indicated two high entropy positions that decomposed into 2 oligotypes (−c 2, −M 20; Figure 4C).

Bottom Line: Proteobacteria were identified as the dominant phylum within both subsurface and thermal spring environments, but only one genera, Rheinheimera, was identified among all samples.Using Morisita similarity indices as a metric for pairwise comparisons between sites, we found that the communities of thermal springs are highly distinct from subsurface datasets.Although the Limpopo thermal springs do not appear to provide a new window for viewing subsurface bacterial communities, we report that the taxonomic compositions of the subsurface sites studied are more similar than previous results would indicate and provide evidence that the microbial communities sampled at depth are more correlated to subsurface conditions than geographical distance.

View Article: PubMed Central - PubMed

Affiliation: Department of Geosciences, Princeton University Princeton, NJ, USA.

ABSTRACT
South Africa has numerous thermal springs that represent topographically driven meteoric water migrating along major fracture zones. The temperature (40-70°C) and pH (8-9) of the thermal springs in the Limpopo Province are very similar to those of the low salinity fracture water encountered in the South African mines at depths ranging from 1.0 to 3.1 km. The major cation and anion composition of these thermal springs are very similar to that of the deep fracture water with the exception of the dissolved inorganic carbon and dissolved O2, both of which are typically higher in the springs than in the deep fracture water. The in situ biological relatedness of such thermal springs and the subsurface fracture fluids that feed them has not previously been evaluated. In this study, we evaluated the microbial diversity of six thermal spring and six subsurface sites in South Africa using high-throughput sequencing of 16S rRNA gene hypervariable regions. Proteobacteria were identified as the dominant phylum within both subsurface and thermal spring environments, but only one genera, Rheinheimera, was identified among all samples. Using Morisita similarity indices as a metric for pairwise comparisons between sites, we found that the communities of thermal springs are highly distinct from subsurface datasets. Although the Limpopo thermal springs do not appear to provide a new window for viewing subsurface bacterial communities, we report that the taxonomic compositions of the subsurface sites studied are more similar than previous results would indicate and provide evidence that the microbial communities sampled at depth are more correlated to subsurface conditions than geographical distance.

No MeSH data available.


Related in: MedlinePlus