# Genome sequence of the obligate gammaproteobacterial methanotroph Methylo microbium album strain BG8.

K Dimitri Kits, Marina G Kalyuzhnaya, Martin G Klotz, Mike S M Jetten, Huub J M Op den Camp, Stéphane Vuilleumier, Françoise Bringel, Alan A Dispirito, J Colin Murrell, D. Bruce, et al.

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K Dimitri Kits, Marina G Kalyuzhnaya, Martin G Klotz, Mike S M Jetten, Huub J M Op den Camp, et al.. Genome sequence of the obligate gammaproteobacterial methanotroph Methylo microbium album strain BG8.. Genome Announcements, 2013, 1 (2), pp.e0017013. 10.1128/genomeA.00170-13 .
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# Genome Sequence of the Obligate Gammaproteobacterial Methanotroph *Methylomicrobium album* Strain BG8

K. Dimitri Kits,ª Marina G. Kalyuzhnaya,ᵇ Martin G. Klotz,ᶜ Mike S. M. Jetten,ᵈ Huub J. M. Op den Camp,ᵈ Stéphane Vuilleumier,ᵉ Françoise Bringel,ᵉ Alan A. DiSpirito,ᵉ J. Colin Murrell,ᵉ D. Bruce,ʰ J.-F. Cheng,¹ A. Copeland,¹ Lynne Goodwin,ʰ Loren Hauser,J Aurélie Lajus,⁴ M. L. Land,¹ A. Lapidus,¹ S. Lucas,¹ Claudine Médigue,⁴ S. Pitluck,¹ Tanja Woyke,¹ A. Zeytun,ʰ Lisa Y. Steinª

Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canadaª; Department of Microbiology, University of Washington, Seattle, Washington, USAᵇ; Department of Biology, University of North Carolina, Charlotte, North Carolina, USAᶜ; Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands⁴; Université de Strasbourg, UMR, CNRS, Strasbourg, Franceᵉ; Department of Biochemistry, Biophysics and Molecular Biology, Ames, Iowa, USA>f; School of Environmental Sciences, University of East Anglia, Norwich, United Kingdomg; Los Alamos National Lab, Los Alamos, New Mexico, USAp; U.S. Department of Energy (DOE), Joint Genome Institute, Walnut Creek, California, USA>; Oak Ridge National Lab, Biosciences Division, Oak Ridge, Tennessee, USAi; Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, Genoscope-IG-CEA, Evry, Francek

The complete genome sequence of *Methylomicrobium album* strain BG8, a methane-oxidizing gammaproteobacterium isolated from freshwater, is reported. Aside from a conserved inventory of genes for growth on single-carbon compounds, *M. album* BG8 carries a range of gene inventories for additional carbon and nitrogen transformations but no genes for growth on multicarbon substrates or for N fixation.

**Received** 7 March 2013 **Accepted** 13 March 2013 **Published** 11 April 2013

**Citation** Kits KD, Kalyuzhnaya MG, Klotz MG, Jetten MSM, Op den Camp HJM, Vuilleumier S, Bringel F, DiSpirito AA, Murrell JC, Bruce D, Cheng J-F, Copeland A, Goodwin L, Hauser L, Lajus A, Land ML, Lapidus A, Lucas S, Médigue C, Pitluck S, Woyke T, Zeytun A, Stein LY. 2013. Genome sequence of the obligate gammaproteobacterial methanotroph *Methylomicrobium album* strain BG8. Genome Announc. 1(2):e00170-13. doi:10.1128/genomeA.00170-13.

**Copyright** © 2013 Kits et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Address correspondence to Lisa Y. Stein, lisa.stein@ualberta.ca.

Methanotrophic bacteria are found in diverse environments and utilize methane as their sole source of energy, reducing tants, and carbon (1). Methanotrophs attenuate the emission of methane, the second most important greenhouse gas (2), and have applications in bioremediation and bioprocessing (3). *Methylomicrobium album* strain BG8 (also known as *Methylobacter albus*, *Methylomonas albus*, and *Methylomonas alba*) is a mesophilic, aerobic gammaproteobacterium isolated from freshwater by Roger Whittenbury et al. (4).

The *M. album* BG8 genome was sequenced, assembled, and annotated by the U.S. Department of Energy Joint Genome Institute (http://www.jgi.doe.gov/sequencing/). Illumina GA II and 454 Titanium standard libraries with paired-end reads were generated, representing 30-fold coverage. Using Newbler v2.3, a chromosomal sequence of 2 contigs and 1 scaffold and a complete plasmid sequence were assembled. Automatic annotation was performed using Prodigal and GenePRIMP (5). The draft genome is 4.49 Mbp, with a mean G+C content of 56.2%. Two copies of the rRNA operon, 42 tRNA genes, and 3,984 predicted protein-coding genes are present. Manual annotation and comparative analysis are under way with assistance from the MicroScope annotation platform at Genoscope (6).

The *M. album* BG8 genome contains one operon (*pmoCAB*) with genes encoding particulate methane monooxygenase and a *pxm* operon (*pxmABC*) with genes encoding a copper membrane monooxygenase of unknown function (7). Genes encoding the enzyme methanol dehydrogenase and accessory proteins (*mxaYDFGIRSAKKL-mxaB*) and a Xox-type methanol dehydrogenase (*xoxFJ*) (8) were identified. Genes encoding enzymes for C₁ metabolism include those for the tetrahydrofolate (H₄-folate) and

tetrahydromethanopterin (H₄MPT)-linked C₁ transfer pathways, glutathione-dependent formaldehyde dehydrogenases (GD-FALDH) and accessory functions, and a NAD-dependent formate dehydrogenase (encoded by *fdh5A*). A membrane-bound formate dehydrogenase (encoded by *fdh3DABC*) is typically absent in strict methanotrophs, but it is expressed in "Candidatus Methyacidiphilum fumariolicum" SolV of the phylum *Verrucomicrobia*. Also similar to "Ca. Methylacidiphilum fumariolicum" SolV, *M. album* BG8 was found to have a complete set of genes for glycogen biosynthesis (9). Genes encoding the complete ribulose monophosphate (RuMP) pathway for formaldehyde assimilation, a complete tricarboxylic acid (TCA) cycle, the pentose phosphate pathway, and the Embden-Meyerhof-Parnas pathway were identified. A complement of genes for a complete serine cycle, with the exception of phosphoenolpyruvate carboxylase, was identified; key genes for the Calvin-Benson-Bassham cycle were absent.

Genes encoding enzymes for nitrogen metabolism were identified, including those for direct ammonium uptake (*amtB*), nitrate transport (*narK*), nitrate or nitrite reduction (*nasCA*, *nasB*, and *nirBD*), and glutamine synthetase/glutamate synthase (*glnA*, *gltB*) and alanine dehydrogenase (*ald*) for ammonium assimilation. Tandem genes encoding proteins implicated in the oxidation of hydroxylamine to nitrite (*haoAB*) were identified, which likely facilitate the detoxification of hydroxylamine produced from the oxidation of ammonia by membrane-bound methane monooxygenase (pMMO) (10). Genes encoding a cytochrome *cd*₁ nitrite reductase (*nirS*) and accessory functions, as well as nitric oxide reductase (*norCB*), were found, perhaps explaining the capacity of this strain to tolerate high nitrite concentrations (11). The *nirS* and *norCB* genes in this strain share high sequence identities with
homologues in other methanotrophs (12, 13). Analysis of the *M. album* BG8 genome sequence enables further understanding of single-carbon metabolism and the environmental adaptation strategies of methanotrophs.

**Nucleotide sequence accession numbers.** The genome sequences of the chromosome and plasmid of *M. album* BG8 have been deposited in GenBank under accession no. CM001475 and CM001476, respectively.

## ACKNOWLEDGMENTS

The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231.

We thank additional members of the Organization for Methanotroph Genome Analysis (OMeGA).

L.Y.S. was supported by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada. M.G.K. was supported by the U.S. NSF (0541797 and 0948202).

## REFERENCES

1. Trotsenko YA, Murrell JC. 2008. Metabolic aspects of aerobic obligate methanotrophy. Adv. Appl. Microbiol. 63:183-229.

2. Conrad R. 2009. The global methane cycle: recent advances in understanding the microbial processes involved. Environ. Microbiol. Rep. 1:285-292.

3. Han JI, Lontoh S, Semrau JD. 1999. Degradation of chlorinated and brominated hydrocarbons by *Methylomicrobium album* BG8. Arch. Microbiol. 172:393-400.

4. Whittenbury R, Phillips KC, Wilkinson JF. 1970. Enrichment, isolation and some properties of methane-utilizing bacteria. J. Gen. Microbiol. 61: 205-218.

5. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119.

6. Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L, Lajus A, Rouy Z, Roche D, Salvignol G, Scarpelli C, Médigue C. 2009. MicroScope: a platform for microbial genome annotation and comparative genomics. Database 2009:bap021. doi:http://dx.doi.org/10.1093/database/bap021.

7. Tavormina PL, Orphan VJ, Kalyuzhnaya MG, Jetten M, Klotz MG. 2011. A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs. Environ. Microbiol. Rep. 3:91-100.

8. Schmidt S, Christen P, Kiefer P, Vorholt JA. 2010. Functional investigation of methanol dehydrogenase-like protein XoxF in *Methylobacterium extorquens* AM1. Microbiology 156:2575-2586.

9. Khadem AF, van Teeseling MCF, Jetten M, Op den Camp HJM, Pol A. 2012. Genomic and physiological analysis of carbon storage in the verrucomicrobial methanotroph "Ca. Methylacidiphilum fumariolicum" SolV. Front. Microbiol. 3:345.

10. Stein LY, Bringel F, DiSpirito AA, Han S, Jetten MS, Kalyuzhnaya MG, Kits KD, Klotz MG, Op den Camp HJ, Semrau JD, Vuilleumier S, Bruce DC, Cheng JF, Davenport KW, Goodwin L, Han S, Hauser L, Lajus A, Land ML, Lapidus A, Lucas S, Médigue C, Pitluck S, Woyke T. 2011. Genome sequence of the methanotrophic alphaproteobacterium *Methylocystis* sp strain Rockwell (ATCC 49242). J. Bacteriol. 193:2668-2669.

11. Nyerges G, Han SK, Stein LY. 2010. Effects of ammonium and nitrite on growth and competitive fitness of cultivated methanotrophic bacteria. Appl. Environ. Microbiol. 76:5648-5651.

12. Svenning MM, Hestnes AG, Wartiainen I, Stein LY, Klotz MG, Kalyuzhnaya MG, Spang A, Bringel F, Vuilleumier S, Lajus A, Médigue C, Bruce DC, Cheng JF, Goodwin L, Ivanova N, Han J, Han CS, Hauser L, Held B, Land ML, Lapidus A, Lucas S, Nolan M, Pitluck S, Woyke T. 2011. Genome sequence of the Arctic methanotroph *Methylobacter tundripaludum* SV96. J. Bacteriol. 193:6418-6419.

13. Boden R, Cunliffe M, Scanlan J, Moussard H, Kits KD, Klotz MG, Jetten MS, Vuilleumier S, Han J, Peters L, Mikhailova N, Teshima H, Tapia R, Kyrpides N, Ivanova N, Pagani I, Cheng JF, Goodwin L, Han C, Hauser L, Land ML, Lapidus A, Lucas S, Pitluck S, Woyke T, Stein L, Murrell JC. 2011. Complete genome sequence of the aerobic marine methanotroph *Methylomonas methanica* MC09. J. Bacteriol. 193: 7001-7002.