Limits...
Comparative metagenomics reveals impact of contaminants on groundwater microbiomes

View Article: PubMed Central

ABSTRACT

To understand patterns of geochemical cycling in pristine versus contaminated groundwater ecosystems, pristine shallow groundwater (FW301) and contaminated groundwater (FW106) samples from the Oak Ridge Integrated Field Research Center (OR-IFRC) were sequenced and compared to each other to determine phylogenetic and metabolic difference between the communities. Proteobacteria (e.g., Burkholderia, Pseudomonas) are the most abundant lineages in the pristine community, though a significant proportion ( >55%) of the community is composed of poorly characterized low abundance (individually <1%) lineages. The phylogenetic diversity of the pristine community contributed to a broader diversity of metabolic networks than the contaminated community. In addition, the pristine community encodes redundant and mostly complete geochemical cycles distributed over multiple lineages and appears capable of a wide range of metabolic activities. In contrast, many geochemical cycles in the contaminated community appear truncated or minimized due to decreased biodiversity and dominance by Rhodanobacter populations capable of surviving the combination of stresses at the site. These results indicate that the pristine site contains more robust and encodes more functional redundancy than the stressed community, which contributes to more efficient nutrient cycling and adaptability than the stressed community.

No MeSH data available.


Predicted geochemical cycling in the FRC subsurface based on metabolic profiles of pristine (FW301, left) and contaminated (FW106, right). The denitrification pathway genes are labeled in bold in the FW106 figure to indicate their overabundance in this metagenome compared to FW301. Dotted lines indicate either that the pathway genes were not detected in the metagenomes, detected in very low abundance, or that bacteria known to implement these pathways were not detected or in extremely low abundance (<1%). Contaminants present in high concentrations at the FW106 site are shown in white boxes. Partitions indicate different geochemical and electrochemical environments that may transiently exist at the OR-IFRC sites and do not necessarily represent the specific environmental partitioning present in these environments.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4628106&req=5

Figure 4: Predicted geochemical cycling in the FRC subsurface based on metabolic profiles of pristine (FW301, left) and contaminated (FW106, right). The denitrification pathway genes are labeled in bold in the FW106 figure to indicate their overabundance in this metagenome compared to FW301. Dotted lines indicate either that the pathway genes were not detected in the metagenomes, detected in very low abundance, or that bacteria known to implement these pathways were not detected or in extremely low abundance (<1%). Contaminants present in high concentrations at the FW106 site are shown in white boxes. Partitions indicate different geochemical and electrochemical environments that may transiently exist at the OR-IFRC sites and do not necessarily represent the specific environmental partitioning present in these environments.

Mentions: Plots in Figures 1 and 3 were generated in Microsoft Excel and modified in Adobe Illustrator to improve fonts and increase legibility. The underlying data was not modified. Figure 2 was generated in iToL and modified in Adobe Illustrator to add labels. The underlying data was not modified. Figure 4 was created entirely in Adobe Illustrator.


Comparative metagenomics reveals impact of contaminants on groundwater microbiomes
Predicted geochemical cycling in the FRC subsurface based on metabolic profiles of pristine (FW301, left) and contaminated (FW106, right). The denitrification pathway genes are labeled in bold in the FW106 figure to indicate their overabundance in this metagenome compared to FW301. Dotted lines indicate either that the pathway genes were not detected in the metagenomes, detected in very low abundance, or that bacteria known to implement these pathways were not detected or in extremely low abundance (<1%). Contaminants present in high concentrations at the FW106 site are shown in white boxes. Partitions indicate different geochemical and electrochemical environments that may transiently exist at the OR-IFRC sites and do not necessarily represent the specific environmental partitioning present in these environments.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4628106&req=5

Figure 4: Predicted geochemical cycling in the FRC subsurface based on metabolic profiles of pristine (FW301, left) and contaminated (FW106, right). The denitrification pathway genes are labeled in bold in the FW106 figure to indicate their overabundance in this metagenome compared to FW301. Dotted lines indicate either that the pathway genes were not detected in the metagenomes, detected in very low abundance, or that bacteria known to implement these pathways were not detected or in extremely low abundance (<1%). Contaminants present in high concentrations at the FW106 site are shown in white boxes. Partitions indicate different geochemical and electrochemical environments that may transiently exist at the OR-IFRC sites and do not necessarily represent the specific environmental partitioning present in these environments.
Mentions: Plots in Figures 1 and 3 were generated in Microsoft Excel and modified in Adobe Illustrator to improve fonts and increase legibility. The underlying data was not modified. Figure 2 was generated in iToL and modified in Adobe Illustrator to add labels. The underlying data was not modified. Figure 4 was created entirely in Adobe Illustrator.

View Article: PubMed Central

ABSTRACT

To understand patterns of geochemical cycling in pristine versus contaminated groundwater ecosystems, pristine shallow groundwater (FW301) and contaminated groundwater (FW106) samples from the Oak Ridge Integrated Field Research Center (OR-IFRC) were sequenced and compared to each other to determine phylogenetic and metabolic difference between the communities. Proteobacteria (e.g., Burkholderia, Pseudomonas) are the most abundant lineages in the pristine community, though a significant proportion ( &gt;55%) of the community is composed of poorly characterized low abundance (individually &lt;1%) lineages. The phylogenetic diversity of the pristine community contributed to a broader diversity of metabolic networks than the contaminated community. In addition, the pristine community encodes redundant and mostly complete geochemical cycles distributed over multiple lineages and appears capable of a wide range of metabolic activities. In contrast, many geochemical cycles in the contaminated community appear truncated or minimized due to decreased biodiversity and dominance by Rhodanobacter populations capable of surviving the combination of stresses at the site. These results indicate that the pristine site contains more robust and encodes more functional redundancy than the stressed community, which contributes to more efficient nutrient cycling and adaptability than the stressed community.

No MeSH data available.