Phylogenomic data support a seventh order of methylotrophic methanogens and provide insights into the evolution of methanogenesis

Genome Biology and Evolution

Volumn 5, Issue 10, 2013, Pages 1769-1780

  Borrel, Guillaume ^a,b   O'Toole, Paul W ^b   Harris, Hugh M B ^b   Peyret, Pierre ^a   Brugère, Jean François ^a   Gribaldo, Simonetta ^c  

^a UNIVERSITÉ CLERMONT AUVERGNE   (France)

^b UNIVERSITY COLLEGE CORK   (Ireland)

^c INSTITUT PASTEUR   (France)

Author keywords

Archaea; Evolution; Genomics; Methanogenesis; Methanomassiliicoccales; Methanoplasmatales

Indexed keywords

RNA 16S;

ARCHAEON; ARTICLE; BIODIVERSITY; DNA SEQUENCE; EVOLUTION; GENETICS; GENOMICS; HUMAN; METHANOGENESIS; METHANOMASSILIICOCCALES; METHANOMICROBIACEAE; METHANOPLASMATALES; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY;

ARCHAEA; EVOLUTION; GENOMICS; METHANOGENESIS; METHANOMASSILIICOCCALES; METHANOPLASMATALES;

BIODIVERSITY; EVOLUTION, MOLECULAR; HUMANS; METHANOMICROBIACEAE; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 84890110026     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evt128     Document Type: Article

References (50)

1. Bapteste E, Brochier C, Boucher Y. 2005. Higher-level classification of the Archaea: evolution of methanogenesis and methanogens. Archaea 1: 353-363.
2. Biderre-Petit C, et al. 2011. Identification of microbial communities involved in the methane cycle of a freshwater meromictic lake. FEMS Microbiol Ecol. 77:533-545.
3. Borrel G, et al. 2012. Genome sequence of "Candidatus Methanomethylophilus alvus" Mx1201, a methanogenic archaea from the human gut belonging to a seventh order of methanogens. J Bacteriol. 194:6944-6945.
4. Bose A, Pritchett MA, Metcalf WW. 2008. Genetic analysis of the methanol-and methylamine-specific methyltransferase 2 genes of Methanosarcina acetivorans C2A. J Bacteriol. 190:4017-4026.
5. Brochier-Armanet C, Forterre P, Gribaldo S. 2011. Phylogeny and evolution of the Archaea: one hundred genomes later. Curr OpinMicrobiol. 14:274-281.
6. Brochier C, Forterre P, Gribaldo S. 2004. Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox. Genome Biol. 5:R17-R17.
7. Criscuolo A, Gribaldo S. 2010. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol. 10:210.
8. Denonfoux J, et al. 2013. Gene capture coupled to high-throughput sequencing as a strategy for targeted metagenome exploration. DNA Res. 20:185-196.
9. Dridi B, Fardeau ML, Ollivier B, Raoult D, Drancourt M. 2012. Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces. Int J Syst Evol Microbiol. 62: 1902-1907.
10. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
11. Evans PN, et al. 2009. Community composition and density of methanogens in the foregut of the Tammar wallaby (Macropus eugenii). Appl Environ Microbiol. 75:2598-2602.
12. Ferguson DJ, Gorlatova N, Grahame DA, Krzycki JA. 2000. Reconstitution of dimethylamine: coenzyme M methyl transfer with a discrete corrinoid protein and two methyltransferases purified from Methanosarcina barkeri. J Biol Chem. 275:29053-29060.
13. Ferguson DJ, Krzycki JA, Grahame DA. 1996. Specific roles of methylcobamide: coenzyme M methyltransferase isozymes in metabolism of methanol and methylamines in Methanosarcina barkeri. J Biol Chem. 271:5189-5194.
14. Fricke WF, et al. 2006. The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis. J Bacteriol. 188:642-658.
15. Gorlas A, Robert C, Gimenez G, Drancourt M, Raoult D. 2012. Complete genome sequence of Methanomassiliicoccus luminyensis, the largest genome of a human-associated Archaea species. J Bacteriol. 194: 4745-4745.
16. Gribaldo S, Brochier-Armanet C. 2006. The origin and evolution of Archaea: a state of the art. Philos Trans R Soc Lond Ser B Biol Sci. 361:1007-1022.
17. Guindon S, et al. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 59:307-321.
18. Hedderich R, WhitmanW. 2006. Physiology and biochemistry of themethane-producing archaea. In: Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E, Dworkin M, editors. Prokaryotes: a Handbook on the Biology of Bacteria. New York: Springer. p. 1050-1079.
19. Horz HP, Seyfarth I, Conrads G. 2012. McrA and 16S rRNA gene analysis suggests a novel lineage of archaea phylogenetically affiliated with Thermoplasmatales in human subgingival plaque. Anaerobe 18: 373-377.
20. Iino T, et al. 2013. Candidatus Methanogranum caenicola: a novel methanogen from the anaerobic digested sludge, and proposal of Methanomassiliicoccaceae fam. nov. and Methanomassiliicoccales ord. nov., for a methanogenic lineage of the class Thermoplasmata. Microb Environ. 28:244-250.
21. Iverson V, et al. 2012. Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science 335: 587-590.
22. Janssen PH, Kirs M. 2008. Structure of the archaeal community of the rumen. Appl Environ Microbiol. 74:3619-3625.
23. Jiang HC, et al. 2008. Dominance of putative marine benthic Archaea in Qinghai Lake, north-western China. EnvironMicrobiol. 10:2355-2367.
24. Jobb G, von Haeseler A, Strimmer K. 2004. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol. 4:18.
25. Kemnitz D, Kolb S, Conrad R. 2005. Phenotypic characterization of Rice Cluster III archaea without prior isolation by applying quantitative polymerase chain reaction to an enrichment culture. Environ Microbiol. 7:553-565.
26. Klenk H-P, et al. 1997. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390:364-370.
27. Lapage SP, et al. 1992. International code of nomenclature of bacteria: bacteriological code, 1990 revision. Washington (DC): ASM Press.
28. Lartillot N, Lepage T, Blanquart S. 2009. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25:2286-2288.
29. Le SQ, Gascuel O. 2008. An improved general amino acid replacement matrix. Mol Biol Evol. 25:1307-1320.
30. Liu Y, Whitman WB. 2008. Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann N Y Acad Sci. 1125:171-189.
31. Lloyd KG, et al. 2013. Predominant archaea in marine sediments degrade detrital proteins. Nature 496:215-218.
32. Meyer F, et al. 2008. The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386.
33. Meyerdierks A, et al. 2010. Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME1 group. Environ Microbiol. 12:422-439.
34. Mihajlovski A, Alric M, Brugere JF. 2008. A putative new order of methanogenic Archaea inhabiting the human gut, as revealed by molecular analyses of the mcrA gene. Res Microbiol. 159:516-521.
35. Mihajlovski A, Dore J, Levenez F, Alric M, Brugere JF. 2010. Molecular evaluation of the human gut methanogenic archaeal microbiota reveals an age-associated increase of the diversity. Environ Microbiol Rep. 2:272-280.
36. Möller-Zinkhan D, Börner G, Thauer R. 1989. Function of methanofuran, tetrahydromethanopterin, and coenzyme F420 in Archaeoglobus fulgidus. Arch Microbiol. 152:362-368.
37. Montzka S, Dlugokencky E, Butler J. 2011. Non-CO2 greenhouse gases and climate change. Nature 476:43-50.
38. Paul K, Nonoh JO, Mikulski L, Brune A. 2012. "Methanoplasmatales, " Thermoplasmatales-related archaea in termite guts and other environments, are the seventh order of methanogens. Appl EnvironMicrobiol. 78:8245-8253.
39. Poulsen M, et al. 2013. Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen. Nat Commun. 4:1428.
40. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
41. Sauer K, Harms U, Thauer RK. 1997. Methanol: coenzymeMmethyltransferase from Methanosarcina barkeri. Eur J Biochem. 243:670-677.
42. Scanlan P, Shanahan F, Marchesi J. 2008. Human methanogen diversity and incidence in healthy and diseased colonic groups usingmcrA gene analysis. BMC Microbiol. 8:79.
43. SprengerWW, van Belzen MC, Rosenberg J, Hackstein J, Keltjens J. 2000. Methanomicrococcus blatticola gen. nov., sp. nov., a methanoland methylamine-reducing methanogen from the hindgut of the cockroach Periplaneta americana. Int J Syst Evol Microbiol. 50: 1989-1999.
44. Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R. 2008. Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol. 6:579-591.
45. van der Lelie D, et al. 2012. The metagenome of an anaerobic microbial community decomposing poplar wood chips. PLoS One 7:e36740.
46. van der Meijden P, et al. 1983. Methyltransferases involved in methanol conversion by Methanosarcina barkeri. Arch Microbiol. 134:238-242.
47. Wassenaar RW, Daas P, Geerts WJ, Keltjens JT, Van der Drift C. 1996. Involvement of methyltransferase-activating protein and methyltransferase 2 isoenzyme II in methylamine: coenzyme M methyltransferase reactions in Methanosarcina barkeri Fusaro. J Bacteriol. 178: 6937-6944.
48. Weiland P. 2010. Biogas production: current state and perspectives. Appl Microbiol Biotechnol. 85:849-860.
49. Welander PV, Metcalf WW. 2005. Loss of the mtr operon in Methanosarcina blocks growth on methanol, but not methanogenesis, and reveals an unknown methanogenic pathway. Proc Natl Acad Sci U S A. 102:10664-10669.
50. Zhu J, et al. 2012. The genome characteristics and predicted function of methyl-group oxidation pathway in the obligate aceticlastic methanogens, Methanosaeta spp. PLoS One 7:e36756.