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The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing.

Mohan AM, Bibby KJ, Lipus D, Hammack RW, Gregory KB - PLoS ONE (2014)

Bottom Line: Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing.Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water.These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection.

View Article: PubMed Central - PubMed

Affiliation: National Energy Technology Laboratory, Pittsburgh, Pennsylvania, United States of America; Department of Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

ABSTRACT
Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. The metabolic profile revealed a relative increase in genes responsible for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection.

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Fraction of genome coverage for source water (SW), produced water day 1 (PW day 1) and produced water day 9 (PW day 9) samples.Reads were mapped against reference genomes using CLC Genomic workbench version 6.5.1 using default parameters. Shown are fractions of reads mapped against each reference genome included in the analysis for all three samples.
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pone-0107682-g003: Fraction of genome coverage for source water (SW), produced water day 1 (PW day 1) and produced water day 9 (PW day 9) samples.Reads were mapped against reference genomes using CLC Genomic workbench version 6.5.1 using default parameters. Shown are fractions of reads mapped against each reference genome included in the analysis for all three samples.

Mentions: Metagenomic reads were mapped against a diverse set of reference genomes to confirm MG-RAST taxonomic results and only reference genomes with good mapping results are discussed in this section. Reference genome mapping results confirmed taxonomic MG-RAST contig analysis. The best mapping results for source water were obtained when sequences were mapped against reference genomes of Alphaproteabacteria, specifically of the order Rhodobacterales (Figures 3, 4). Similarly, produced water day 1 sample mapping results suggest that it was dominated by bacteria of the orders Rhodobacterales and Thermoanaerobacterales (Figures 3, 4). A distinct shift in bacterial community was observed between produced water day 1 samples and produced water day 9 samples based on mapping results. Best mapping results for produced water day 9 samples were obtained for reference genomes in the order Campylobacterales and Alteromondales further supporting the MG-RAST results (Figures 3, 4). Produced water samples demonstrated a distinctive signature with reads mapping best to few select reference genomes, while source water sample reads were distributed more evenly throughout all included reference genomes. For four reference genomes (Thermoanaerobacter sp. X514, Thermoanaerobacter pseudethanolicus, Thermoanaerobacter mathranii in produced water day 1 samples and Marinobacter hydrocarbonoclasticus DSM 7299 in produced water day 9 sample) more than 80% coverage was achieved suggesting that these species could play important roles in the microbial community of the representative sample (Figure 3). Highest observed reference genome coverage for source water sample sequences were 79% for Roseovarius sp. 217, 40% for Ruegeria pomeroyi and 38% for Rhodobacter sphaeroides (Figure 3). For produced water day 1 samples, about 10% of all trimmed sequencing reads mapped against the three Thermanaerobacter genomes included in the analysis and 8–13% of reads mapped successfully against Roseovarius sp. 217 and Roseovarius nubinhibens genomes (Figure 4). 7.7% of produced water day 1 reads mapped against the Ruegeria pomeroyi genome (Figure 4). 4–6% of reads for produced water day 9 samples mapped against two different Marinobacter and Arcobacter reference genomes and one Vibrio reference genome (Figure 4). Almost 16% of all reads from source water samples mapped against Roseovarius sp. 217 and approximately 4–6% of reads for source water sample mapped against each Dinoroseobacter shibae, Ruegeria pomeroyi, Rhodobacter sphaeroides and Rhodobacter capsulatus genomes (Figure 4). All mapping results are summarized in Table S3. The high number of reads form source water and produced water day 1 samples mapping against Roseovarius species is in agreement with previous 16S rRNA gene sequencing [5], implying the Roseovarius species might be of importance in these waters. Roseovarius sp. was previously identified in natural gas brines from the Marcellus shale and its potential implications are discussed elsewhere [9].


The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing.

Mohan AM, Bibby KJ, Lipus D, Hammack RW, Gregory KB - PLoS ONE (2014)

Fraction of genome coverage for source water (SW), produced water day 1 (PW day 1) and produced water day 9 (PW day 9) samples.Reads were mapped against reference genomes using CLC Genomic workbench version 6.5.1 using default parameters. Shown are fractions of reads mapped against each reference genome included in the analysis for all three samples.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4206270&req=5

pone-0107682-g003: Fraction of genome coverage for source water (SW), produced water day 1 (PW day 1) and produced water day 9 (PW day 9) samples.Reads were mapped against reference genomes using CLC Genomic workbench version 6.5.1 using default parameters. Shown are fractions of reads mapped against each reference genome included in the analysis for all three samples.
Mentions: Metagenomic reads were mapped against a diverse set of reference genomes to confirm MG-RAST taxonomic results and only reference genomes with good mapping results are discussed in this section. Reference genome mapping results confirmed taxonomic MG-RAST contig analysis. The best mapping results for source water were obtained when sequences were mapped against reference genomes of Alphaproteabacteria, specifically of the order Rhodobacterales (Figures 3, 4). Similarly, produced water day 1 sample mapping results suggest that it was dominated by bacteria of the orders Rhodobacterales and Thermoanaerobacterales (Figures 3, 4). A distinct shift in bacterial community was observed between produced water day 1 samples and produced water day 9 samples based on mapping results. Best mapping results for produced water day 9 samples were obtained for reference genomes in the order Campylobacterales and Alteromondales further supporting the MG-RAST results (Figures 3, 4). Produced water samples demonstrated a distinctive signature with reads mapping best to few select reference genomes, while source water sample reads were distributed more evenly throughout all included reference genomes. For four reference genomes (Thermoanaerobacter sp. X514, Thermoanaerobacter pseudethanolicus, Thermoanaerobacter mathranii in produced water day 1 samples and Marinobacter hydrocarbonoclasticus DSM 7299 in produced water day 9 sample) more than 80% coverage was achieved suggesting that these species could play important roles in the microbial community of the representative sample (Figure 3). Highest observed reference genome coverage for source water sample sequences were 79% for Roseovarius sp. 217, 40% for Ruegeria pomeroyi and 38% for Rhodobacter sphaeroides (Figure 3). For produced water day 1 samples, about 10% of all trimmed sequencing reads mapped against the three Thermanaerobacter genomes included in the analysis and 8–13% of reads mapped successfully against Roseovarius sp. 217 and Roseovarius nubinhibens genomes (Figure 4). 7.7% of produced water day 1 reads mapped against the Ruegeria pomeroyi genome (Figure 4). 4–6% of reads for produced water day 9 samples mapped against two different Marinobacter and Arcobacter reference genomes and one Vibrio reference genome (Figure 4). Almost 16% of all reads from source water samples mapped against Roseovarius sp. 217 and approximately 4–6% of reads for source water sample mapped against each Dinoroseobacter shibae, Ruegeria pomeroyi, Rhodobacter sphaeroides and Rhodobacter capsulatus genomes (Figure 4). All mapping results are summarized in Table S3. The high number of reads form source water and produced water day 1 samples mapping against Roseovarius species is in agreement with previous 16S rRNA gene sequencing [5], implying the Roseovarius species might be of importance in these waters. Roseovarius sp. was previously identified in natural gas brines from the Marcellus shale and its potential implications are discussed elsewhere [9].

Bottom Line: Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing.Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water.These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection.

View Article: PubMed Central - PubMed

Affiliation: National Energy Technology Laboratory, Pittsburgh, Pennsylvania, United States of America; Department of Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

ABSTRACT
Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. The metabolic profile revealed a relative increase in genes responsible for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection.

Show MeSH