- Open Access
Complete genome sequence of Methanocorpusculum labreanum type strain Z
Standards in Genomic Sciences volume 1, pages197–203(2009)
Methanocorpusculum labreanum is a methanogen belonging to the order Methanomicrobiales within the archaeal phylum Euryarchaeota. The type strain Z was isolated from surface sediments of Tar Pit Lake in the La Brea Tar Pits in Los Angeles, California. M. labreanum is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. labreanum type strain Z and its annotation. This is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea.
Methanocorpusculum labreanum is a methanogen belonging to the order Methanomicrobiales within the archaeal kingdom Euryarchaeota. Strain Z is the type strain of this species. It was isolated from surface sediments of Tar Pit Lake at the La Brea Tar Pits in Los Angeles . Most of the other described members of this family have been isolated from anaerobic digesters or waste water . The genus covers organisms with a wide temperature range. One psychrotolerant strain was isolated from a Russian pond polluted with paper mill waste water , while other strains were found in heated sediment at a hydrothermal vent site . Methanocorpusculum species may be common in subsurface environments as they were the most prominent genus found in a coal bed in Indiana  and in shale in northern Michigan .
Methanogens have been divided into two groups known as Class I and Class II based on phylogeny . Class I includes the orders Methanococcales, Methanobacteriales, and Methanopyrales, which use H2/CO2 or formate as substrates for methanogenesis, although some can also use alcohols as electron donors. Class II includes the orders Methanosarcinales and Methanomicrobiales. Some of the Methanosarcinales are capable of using various methyl compounds as substrates for methanogenesis including acetate, methylamines, and methanol, but Methanomicrobiales are restricted to the same substrates as the Class I methanogens . Therefore, Methanomicrobiales are phylogenetically closer to Methanosarcinales but physiologically more similar to Class I methanogens, making them an interesting target for genome sequencing. In a 2006 Community Sequencing Program (CSP) project, we proposed sequencing two members of the order Methanomicrobiales: M. labreanum and Methanoculleus marisnigri. Previously only one genome was available from this order, that of Methanospirillum hungatei. Methanocorpusculum labreanum and Methanoculleus marisnigri are phylogenetically distant from each other and from Methanospirillum hungatei (Figure 1), and they represent the three families within the order Methanomicrobiales. We report here the sequence and annotation of M. labreanum type strain Z.
Classification and features
Methanocorpusculum labreanum Z was isolated from surface sediments at the La Brea Tar Pits . A polypropylene bottle was filled with half surface sediment and half lake water. In an anaerobic chamber the contents of the bottle were mixed to suspend the sediment, and 0.5 ml of the slurry was added to 5 ml enrichment medium. The enrichment medium contained sodium formate, trypticase peptone, and salts. The gas phase was H2-CO2 at a ratio of 4:1 and a pressure of 152 kPa. The physiological characteristics of M. labreanum were described as follows . The cells were coccoid with a diameter of 0.4–2.0 µm. They were irregular in shape under some growth conditions, such as higher salt or with added acetate. Motility was not observed and no flagella were observed. Growth was observed on H2/CO2 or formate, but not with acetate, propionate, methanol, trimethylamine, or ethanol. Growth was observed in a narrow window of pH, from 6.5 to 7.5, with pH 7.0 as the optimal value. Growth was observed between 25 and 40°C, with an optimum at 37°C. M. labreanum can tolerate a wide range of salt concentration, from 0 to 30 g/L NaCl. Acetate was stimulatory at lower salt concentrations. Either trypticase peptone, yeast extract, or cysteine was required for growth. The features of M. labreanum Z are presented in Table 1.
Genome sequencing information
Genome project history
M. labreanum was selected for sequencing based upon its phylogenetic position relative to other methanogens of the order Methanomicrobiales. It is part of a 2006 Joint Genome Institute Community Sequencing Program project that included six diverse archaeal genomes. A summary of the project information is shown in Table 2. The complete genome sequence was finished in January, 2007. The GenBank accession number for the project is CP000559. The genome project is listed in the Genomes OnLine Database (GOLD)  as project Gc00506. Sequencing was carried out at the Joint Genome Institute (JGI) Production Genomics Facility (PGF). Quality assurance was done by JGI-Stanford. Finishing was done at JGI-PGF. Annotation was done by JGI-Oak Ridge National Laboratory (ORNL) and by JGI-PGF.
Growth conditions and DNA isolation
The methods for DNA isolation, genome sequencing and assembly for this genome have previously been published .
Protein-coding genes were identified using a combination of CRITICA  and Glimmer  followed by a round of manual curation using the JGI GenePRIMP pipeline . GenePRIMP points out cases where gene start sites may be incorrect based on alignment with homologous proteins. It also highlights genes that appear to be broken into two or more pieces, due to a premature stop codon or frameshift, and genes that are disrupted by transposable elements. All of these types of broken and interrupted genes are labeled as pseudogenes. Genes that may have been missed by the gene calling programs are also identified in intergenic regions. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Signal peptides were identified with SignalP , and transmembrane helices were determined with TMHMM . CRISPR elements were identified with the CRISPR Recognition Tool (CRT) . Paralogs are hits of a protein against another protein within the same genome with an e-value of 10−2 or lower. The tRNAScanSE tool  was used to find tRNA genes. Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes Expert Review (IMG-ER) platform .
The genome of M. labreanum Z consists of a single circular chromosome (Figure 2). The genome size of 1.80 Mbp is similar to those of Class I methanogens, but smaller than the genomes of Methanosarcina species and the other Methanomicrobiales, which range between 2.5 and 5.8 Mbp. The G+C percentage is 50.0%, higher than that of most other sequenced methanogens. There are 1,830 genes, of which 1,765 are protein-coding genes and the remaining 65 are RNA genes. There were only 26 pseudogenes identified, constituting 1.4% of the total genes. The properties and statistics of the genome are summarized in Table 3, and genes belonging to COG functional categories are listed in Table 4.
Insights from the genome sequence
The genome sequence of M. labreanum Z shows some similarities to Class I methanogens and some to Methanosarcinales but also has some unique features. In common with Class I methanogens, M. labreanum uses a partial reductive TCA cycle to synthesize 2-oxoglutarate, and it has the Eha membrane-bound hydrogenase. Similar to Methanosarcinales, M. labreanum has the Ech membrane-bound hydrogenase. A unique feature of M. labreanum and the other Methanomicrobiales is the presence of anti- and anti-anti-sigma factors, which is surprising as Archaea do not use sigma factors. Phylogenetic analysis of methanogenesis and cofactor biosynthesis enzymes suggest that Methanomicrobiales form a group distinct from other methanogens, and therefore methanogens can be split in to three classes . Surprisingly M. labreanum lacks the F420-nonreducing hydrogenase, which has been proposed to couple Coenzyme M-Coenzyme B heterodisulfide reduction and ferredoxin reduction for the first step of methanogenesis in the cytoplasm of Methanomicrobiales . In place of this hydrogenase, M. labreanum may use the membrane-bound hydrogenase Mbh or energy-converting hydrogenase Ech to couple heterodisulfide reduction to a transmembrane ion gradient .
Zhao Y, Boone DR, Mah RA, Boone JE, Xun L. Isolation and characterization of Methanocorpusculum labreanum sp. nov. from the LaBrea Tar Pits. Int J Syst Bacteriol 1989; 39:10–13.
Garcia JL, Ollivier B, Whitman WB. The order Methanomicrobiales. Prokaryotes 2006; 3:208–230. doi:10.1007/0-387-30743-5 10
Simankova MV, Kotsyurbenko OR, Lueders T, Nozhevnikova AN, Wagner B, Conrad R, Friedrich MW. Isolation and characterization of new strains of methanogens from cold terrestrial habitats. Syst Appl Microbiol 2003; 26:312–318. PubMed doi:10.1078/072320203322346173
Dhillon A, Lever M, Lloyd KG, Albert DB, Sogin ML, Teske A. Methanogen diversity evidenced by molecular characterization of methyl coenzyme M reductase A (mcrA) genes in hydrothermal sediments of the Guaymas Basin. Appl Environ Microbiol 2005; 71:4592–4601. PubMed doi:10.1128/AEM.71.8.4592-4601.2005
Strąpoć D, Picardal FW, Turich C, Schaperdoth I, Macalady JL, Lipp JS, Lin YS, Ertefai TF, Schubotz F, Hinrichs KU, et al. Methane-producing microbial community in a coal bed of the Illinois basin. Appl Environ Microbiol 2008; 74:2424–2432. PubMed doi:10.1128/AEM.02341-07
Waldron PJ, Petsch ST, Martini AM, Nüsslein K. Salinity constraints on subsurface archaeal diversity and methanogenesis in sedimentary rock rich in organic matter. Appl Environ Microbiol 2007; 73:4171–4179. PubMed doi:10.1128/AEM.02810-06
Bapteste É, Brochier C, Boucher Y. Higher-level classification of the Archaea: evolution of methanogenesis and methanogens. Archaea 2005; 1:353–363. PubMed doi:10.1155/2005/859728
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, et al. The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 2009; 37:D141–D145. PubMed doi:10.1093/nar/gkn879
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541–547. PubMed doi:10.1038/nbt1360
Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576–4579. PubMed doi:10.1073/pnas.87.12.4576
Balch WE, Fox GE, Magrum LJ, Woese CR, Wolfe RS. Methanogens: reevaluation of a unique biological group. Microbiol Rev 1979; 43: 260–296. PubMed
List Editor. Validation List no. 6. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. Int J Syst Bacteriol 1981; 31: 215–218.
Garrity GM, Holt JG. Phylum AII. Euryarchaeota phy. nov. In Bergey’s Manual of Systematic Bacteriology, vol. 1. 2nd ed. Edited by: Garrity, GM, Boone, DR and Castenholz, RW. Springer, New York; 2001:211–355.
List Editor. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Validation List no. 85. Int J Syst Evol Microbiol 2002; 52: 685–690. PubMed doi:10.1099/ijs.0.02358-0
Garrity GM, Bell JA, Lilburn T. The revised road map to the manual. In: Brenner, DJ, Kreig, NR, Staley, JT Eds. 2009. Bergey’s Manual of Systematic Bacteriology, 2nd Ed. Vol 2 The Proteobacteria Part A Introductory Essays. 2005 pp 159–220
Balch WE, Fox GE, Magrum LJ, Woese CR, Wolfe RS. Methanogens: reevaluation of a unique biological group. Microbiol Rev 1979; 43:260–296. PubMed
Editor L. Validation List no 30. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. Int J Syst Bacteriol 1989; 39: 371.
Zellner G, Stackebrandt E, Messner P, Tindall BJ, Conway de Macario E, Kneifel H, Sleytr UB, Winter J. Methanocorpusculaceae fam. nov., represented by Methanocorpusculum parvum, Methanocorpusculum sinense spec. nov. and Methanocorpusculum bavaricum spec. nov. Arch Microbiol 1989; 151: 381–390. PubMed doi:10.1007/BF00416595
Xun L, Boone DR, Mah RA. Deoxyribonucleic acid hybridization study of Methanogenium and Methanocorpusculum species, emendation of the genus Methanocorpusculum, and transfer of Methanogenium aggregans to the genus Methanocorpusculum as Methanocorpusculum aggregans comb. nov. Int J Syst Bacteriol 1989; 39:109–111.
Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes OnLine Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2008; 36:D475–D479. PubMed doi:10.1093/nar/gkm884
Anderson I, Ulrich LE, Lupa B, Susanti D, Porat I, Hooper SD, Lykidis A, Sieprawska-Lupa M, 0020Dharmarajan L, Goltsman E, et al. Genomic characterization of Methanomicrobiales reveals three classes of methanogens. PLoS ONE 2009; 4:e5797. PubMed doi:10.1371/journal.pone.0005797
Badger JH, Olsen GJ. CRITICA: coding region identification tool invoking comparative analysis. Mol Biol Evol 1999; 16:512–524. PubMed
Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999; 27:4636–4641. PubMed doi:10.1093/nar/27.23.4636
Pati A. GenePRIMP: A Gene Prediction Improvement Pipeline for microbial genomes. (Submitted).
Emanuelsson O, Brunak S, von Heijne G, Nielsen H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2007; 2:953–971. PubMed doi:10.1038/nprot.2007.131
Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001; 305:567–580. PubMed doi:10.1006/jmbi.2000.4315
Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 2007; 8:209. PubMed doi:10.1186/1471-2105-8-209
Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964. PubMed doi:10.1093/nar/25.5.955
Markowitz VM, Mavromatis K, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271–2278 PubMed doi:10.1093/bioinformatics/btp393
Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R. Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol 2008; 6:579–591. PubMed doi:10.1038/nrmicro1931
This work was performed under the auspices of the US Department of Energy’s Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under Contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under Contract No. DE-AC02-06NA25396. L. H. and M. L. were supported by the Department of Energy under contract DE-AC05-000R22725. M. S.-L., and W. B. W. were supported by DOE contract number DE-FG02-97ER20269.
About this article
Cite this article
Anderson, I.J., Sieprawska-Lupa, M., Goltsman, E. et al. Complete genome sequence of Methanocorpusculum labreanum type strain Z. Stand in Genomic Sci 1, 197–203 (2009) doi:10.4056/sigs.35575