Metagenome-Assembled Genome Sequence of Pseudomonas stutzeri Strain CO183 Isolated from a Coalbed Methane Well

A near-complete Pseudomonas stutzeri draft genome was extracted from a coalbed metagenome. The draft genome described herein provides insight into the functional pathways encoded by this bacterium and its potential role in coalbed methane environments.

supplies necessitates alternative methods to maximize utilization of these supplies. One alternative method, microbialenhanced coalbed methane, harnesses resident microbial populations for in situ natural gas production from unmineable coal seams (1). The Pseudomonas stutzeri strain CO183 draft genome was extracted from the assembled metagenome of coalbed methane cuttings. The sub-bituminous coal samples were retrieved from the Basal Coal Zone at a depth of 730 m. DNA extraction was performed by An and coworkers, as described previously (2). Illumina paired-end read data used in this study was obtained from the Hydrocarbon Metagenome Project database (http://hmp .ucalgary.ca).
Metagenome reads were assembled with metaSPAdes (3), binned with VizBin (4), and the most complete genome bin was assigned to the genus Pseudomonas. Specifically, metagenome contigs were mapped to multiple P. stutzeri strains (5), and a total of 866 contigs (4,740,859 bp) were mapped to P. stutzeri RCH2 (E-value cutoff ϭ 1e Ϫ20 ). Using 833 Pseudomonas-specific marker genes in CheckM (6), the resultant genome bin was 92.84% complete and had 13.64% contamination. The mapped Pseudomonasassigned contigs and the raw metagenome reads were used as input for paired-read iterative contig extension (PRICE) (7), and after 30 cycles the genome bin improved significantly, resulting in a bin of 117 contigs (4,522,918 bp) at 99.27% completeness and 0.4% contamination. The longest contig was 280,110 bp, the N 50 was 74,098, and the GC content was 62.97%. The final draft genome bin had an average nucleotide identity of 97.59% with P. stutzeri RCH2.
The genome was annotated with Rapid Annotations using Subsystem Technology (RAST) version 2.0 using the RASTtk pipeline (8,9) and the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAP) (http://www.ncbi.nlm.nih.gov/genome/annotation _prok). RAST estimated 4,396 coding sequences and 64 RNAs. PGAP estimated 4,429 total genes (4,066 coding genes), 68 RNA genes (four rRNAs, 60 tRNAs, and four ncRNAs), and 115 pseudogenes. Initial analysis suggests that the genome encodes for a complete tricarboxylic acid cycle, heavy-metal resistance (copper, chromium, cadmium, zinc, arsenic), and denitrification pathways. Future comparative analyses of Pseudomonas stutzeri strain CO183 with other Pseudomonas spp. found in coalbed methane environments will provide insight into the ecology of these strains, how they evolved, and their contribution to biogenic coal degradation.
Accession number(s). This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number MCNJ00000000. The version described in this paper is the first version, MCNJ01000000.

ACKNOWLEDGMENTS
This technical effort was performed in support of the National Energy Technology Laboratory's ongoing research under the RES contract DE-FE0004000.
This project was funded by the Department of Energy, National Energy Technology Laboratory, an agency of the United States Government, through a support contract with AECOM. Neither the United States Government nor any agency thereof, nor any of their employees, nor AECOM, nor any of their employees, makes any warranty, expressed or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.

FUNDING INFORMATION
This work, including the efforts of Daniel E. Ross and Djuna Gulliver, was funded by RES contract to NETL (DE-FE0004000).