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Genome Announc. 2017 March; 5(11): e00033-17.
Published online 2017 March 16. doi:  10.1128/genomeA.00033-17
PMCID: PMC5356057

Draft Genome Sequence of Pseudomonas sp. BDAL1 Reconstructed from a Bakken Shale Hydraulic Fracturing-Produced Water Storage Tank Metagenome

ABSTRACT

We report the 5,425,832 bp draft genome of Pseudomonas sp. strain BDAL1, recovered from a Bakken shale hydraulic fracturing-produced water tank metagenome. Genome annotation revealed several key biofilm formation genes and osmotic stress response mechanisms necessary for survival in hydraulic fracturing-produced water.

GENOME ANNOUNCEMENT

Microbial activity associated with hydraulic fracturing-produced water and subsequently the hydraulic fracturing infrastructure is considered a significant operational concern due to the potential for corrosion, souring, and biofouling (1,4). Several studies have recently investigated the microbial community structure associated with hydraulic fracturing-produced water and hydraulic fracturing facilities (1, 5, 6). These investigations have provided interesting insights into the taxonomy of microbial populations associated with these environments. However, little is known about the functional potential and metabolic ability of these microorganisms that may result in interference with hydraulic fracturing operations.

Here, we present the draft genome of Pseudomonas sp. strain BDAL1, assembled from the metagenome of Bakken shale hydraulic fracturing-produced water, sampled from a produced water storage tank. Sequencing libraries were prepared using Illumina Nextera XT and sequenced using Illumina MiSeq technology (Illumina, San Diego, CA). Sequencing reads were quality trimmed (Q30) and de novo assembled into contigs using CLC-Genomics-Workbench version 8.5.1 (http://www.clcbio.com/products/clc-genomics-workbench) and SPAdes version 3.5.1 (7). Assembled contigs were grouped into genome bins with Vizbin (8) and taxonomy assessed with PhyloPythia (9). Metagenomic reads were mapped against binned contigs and reassembled using SPAdes.

The final draft genome contained 128 contigs of 5000 bp to 243,670 bp in length and an N50 of 63,183 bp. The total genome size was 5,425,832 bp with a mean G+C content of 58.4% and had an average of 19-fold coverage. Draft genome completeness and contamination were estimated using 833 Pseudomonas marker genes in CheckM (10). The final draft genome was found to be 97.4% complete and contain 0.4% contamination.

The draft genome was annotated by Rapid Annotations using Subsystems Technology (RAST) (11, 12) revealing 4,998 gene coding sequences (CDs) and 51 RNA sequences (48 tRNA, 16S, 23S, and 5S rRNA). Phylogenetic analysis of the recovered 16S rRNA gene sequence using BLASTn suggested that Pseudomonas sp. strain BDAL1 is closely related to Pseudomonas syringae pv. phaseolicola 1448A. Whole-genome alignment using an average nucleotide identity calculator confirmed the close phylogenetic relationship (99.9% nucleotide identity) (13, 14). RAST (11, 12) annotation allowed the discovery of genes participating in biofilm formation processes. These included members of the alg family involved in alginate metabolism and the levan production gene levansucrase (15, 16). Furthermore, multiple genes of the polysaccharide synthase locus psl and the glycerol transferase glt2, involved in exopolysaccharide (EPS) production were identified (16, 17). Annotation also allowed the identification of the osmotic stress response genes ProX, ProU, and the Trk complex suggesting the potential for potassium ion uptake and osmoprotectant accumulation.

The recovery and analysis of the Pseudomonas sp. BDAL1 draft genome revealed a high number of biofilm formation genes, suggesting significant potential for biofilm formation and biofouling events in hydraulic fracturing-produced water storage tank and other parts of the hydraulic fracturing infrastructure. More detailed analysis of this and other bacterial genomes recovered from hydraulic fracturing environments will lead to a better understanding of microbial activity in these environments.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number MCRW00000000. The version described in this paper is version MCRW01000000.

ACKNOWLEDGMENTS

This technical effort was performed under the RES contract RES1000027/183U and was supported by the Oak Ridge Institute of Science and Education (ORISE).

Footnotes

Citation Lipus D, Ross D, Bibby K, Gulliver D. 2017. Draft genome sequence of Pseudomonas sp. BDAL1 reconstructed from a Bakken shale hydraulic fracturing-produced water storage tank metagenome. Genome Announc 5:e00033-17. https://doi.org/10.1128/genomeA.00033-17.

REFERENCES

1. Cluff MA, Hartsock A, MacRae JD, Carter K, Mouser PJ 2014. Temporal changes in microbial ecology and geochemistry in produced water from hydraulically fractured Marcellus Shale gas wells. Environ Sci Technol 48:6508–6517. doi:.10.1021/es501173p [PubMed] [Cross Ref]
2. Kargbo DM, Wilhelm RG, Campbell DJ 2010. Natural gas plays in the Marcellus shale: challenges and potential opportunities. Environ Sci Technol 44:5679–5684. doi:.10.1021/es903811p [PubMed] [Cross Ref]
3. Gregory KB, Vidic RD, Dzombak DA 2011. Water management challenges associated with the production of shale gas by hydraulic fracturing. Elements 7:181–186. doi:.10.2113/gselements.7.3.181 [Cross Ref]
4. Vengosh A, Jackson RB, Warner N, Darrah TH, Kondash A 2014. A critical review of the risks to water resources from unconventional shale gas development and hydraulic fracturing in the United States. Environ Sci Technol 48:8334–8348. doi:.10.1021/es405118y [PubMed] [Cross Ref]
5. Murali Mohan A, Hartsock A, Bibby KJ, Hammack RW, Vidic RD, Gregory KB 2013. Microbial community changes in hydraulic fracturing fluids and produced water from shale gas extraction. Environ Sci Technol 47:13141–13150. doi:.10.1021/es402928b [PubMed] [Cross Ref]
6. Murali Mohan AM, Hartsock A, Hammack RW, Vidic RD, Gregory KB 2013. Microbial communities in flowback water impoundments from hydraulic fracturing for recovery of shale gas. FEMS Microbiol Ecol 86:567–580. doi:.10.1111/1574-6941.12183 [PubMed] [Cross Ref]
7. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi:.10.1089/cmb.2012.0021 [PMC free article] [PubMed] [Cross Ref]
8. Laczny CC, Sternal T, Plugaru V, Gawron P, Atashpendar A, Margossian HH, Coronado S, der Maaten Lv, Vlassis N, Wilmes P 2015. VizBin-an application for reference-independent visualization and human-augmented binning of metagenomic data. Microbiome 3:1. doi:.10.1186/s40168-014-0066-1 [PMC free article] [PubMed] [Cross Ref]
9. McHardy AC, Martín HG, Tsirigos A, Hugenholtz P, Rigoutsos I 2007. Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods 4:63–72. doi:.10.1038/nmeth976 [PubMed] [Cross Ref]
10. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. doi:.10.1101/gr.186072.114 [PubMed] [Cross Ref]
11. Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards R 2008. The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386. doi:.10.1186/1471-2105-9-386 [PMC free article] [PubMed] [Cross Ref]
12. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R 2014. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42:D206–D214. doi:.10.1093/nar/gkt1226 [PMC free article] [PubMed] [Cross Ref]
13. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM 2007. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91. doi:.10.1099/ijs.0.64483-0 [PubMed] [Cross Ref]
14. Rodriguez-R LM, Konstantinidis KT 2014. Bypassing cultivation to identify bacterial species. Microbe 9:111–118. doi:.10.1128/microbe.9.111.1 [Cross Ref]
15. Laue H, Schenk A, Li H, Lambertsen L, Neu TR, Molin S, Ullrich MS 2006. Contribution of alginate and levan production to biofilm formation by Pseudomonas syringae. Microbiology 152:2909–2918. doi:.10.1099/mic.0.28875-0 [PubMed] [Cross Ref]
16. Mann EE, Wozniak DJ 2012. Pseudomonas biofilm matrix composition and niche biology. FEMS Microbiol Rev 36:893–916. doi:.10.1111/j.1574-6976.2011.00322.x [PMC free article] [PubMed] [Cross Ref]
17. Flemming H-C, Wingender J 2010. The biofilm matrix. Nat Rev Microbiol 8:623–633. doi:.10.1038/nrmicro2415 [PubMed] [Cross Ref]

Articles from Genome Announcements are provided here courtesy of American Society for Microbiology (ASM)