Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis

[1]  Kaiyuan Zheng,et al.  The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea , 2016, Science.

[2]  Donovan H. Parks,et al.  Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota , 2016, Nature Microbiology.

[3]  S. Gribaldo,et al.  Methanogenesis and the Wood–Ljungdahl Pathway: An Ancient, Versatile, and Fragile Association , 2016, Genome biology and evolution.

[4]  E. Koonin,et al.  Diversity and Evolution of Type IV pili Systems in Archaea , 2016, Front. Microbiol..

[5]  Wen-Tso Liu,et al.  Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen , 2016, The ISME Journal.

[6]  W. Whitman.  Bergey's Manual of Systematics of Archaea and Bacteria , 2016 .

[7]  Donovan H. Parks,et al.  Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics , 2015, Science.

[8]  M. V. van Loosdrecht,et al.  Methanosalsum natronophilum sp. nov., and Methanocalculus alkaliphilus sp. nov., haloalkaliphilic methanogens from hypersaline soda lakes. , 2015, International journal of systematic and evolutionary microbiology.

[9]  G. Garrity,et al.  Euryarchaeota phy. nov. , 2015 .

[10]  G. Muyzer,et al.  Functional microbiology of soda lakes. , 2015, Current opinion in microbiology.

[11]  M. V. van Loosdrecht,et al.  Methanogenesis at extremely haloalkaline conditions in the soda lakes of Kulunda Steppe (Altai, Russia). , 2015, FEMS microbiology ecology.

[12]  Kira S. Makarova,et al.  Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales , 2015, Life.

[13]  R. Daniel,et al.  New Mode of Energy Metabolism in the Seventh Order of Methanogens as Revealed by Comparative Genome Analysis of “Candidatus Methanoplasma termitum” , 2014, Applied and Environmental Microbiology.

[14]  K. Schleifer,et al.  Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences , 2014, Nature Reviews Microbiology.

[15]  S. Gribaldo,et al.  Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine , 2014, BMC Genomics.

[16]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[17]  A. Oren.  Life at high salt concentrations, intracellular KCl concentrations, and acidic proteomes , 2013, Front. Microbiol..

[18]  S. Gribaldo,et al.  Phylogenomic Data Support a Seventh Order of Methylotrophic Methanogens and Provide Insights into the Evolution of Methanogenesis , 2013, Genome biology and evolution.

[19]  E. Koonin,et al.  Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park , 2013, Biology Direct.

[20]  S. Haruta,et al.  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 , 2013, Microbes and environments.

[21]  E. Koonin,et al.  Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer , 2012, Biology Direct.

[22]  H. Atomi,et al.  Enzymatic Characterization of AMP Phosphorylase and Ribose-1,5-Bisphosphate Isomerase Functioning in an Archaeal AMP Metabolic Pathway , 2012, Journal of bacteriology.

[23]  A. Brune,et al.  “Methanoplasmatales,” Thermoplasmatales-Related Archaea in Termite Guts and Other Environments, Are the Seventh Order of Methanogens , 2012, Applied and Environmental Microbiology.

[24]  B. Dridi,et al.  Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces. , 2012, International journal of systematic and evolutionary microbiology.

[25]  A. Oren,et al.  The amino acid composition of proteins from anaerobic halophilic bacteria of the order Halanaerobiales , 2012, Extremophiles.

[26]  J. Chanton,et al.  Substrate limitation for methanogenesis in hypersaline environments. , 2012, Astrobiology.

[27]  Natalya Yutin,et al.  Phylogenomics of prokaryotic ribosomal proteins , 2011, Genome Biology.

[28]  Ramón Doallo,et al.  ProtTest 3: fast selection of best-fit models of protein evolution , 2011, Bioinform..

[29]  Ramón Doallo,et al.  ProtTest-HPC: Fast Selection of Best-Fit Models of Protein Evolution , 2010, Euro-Par Workshops.

[30]  O. Gascuel,et al.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.

[31]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[32]  K. Timmis.  Handbook of hydrocarbon and lipid microbiology , 2010 .

[33]  R. Conrad,et al.  The global methane cycle: recent advances in understanding the microbial processes involved. , 2009, Environmental microbiology reports.

[34]  P. Pevzner,et al.  False discovery rates of protein identifications: a strike against the two-peptide rule. , 2009, Journal of proteome research.

[35]  A. Baines.  Evolution of spectrin function in cytoskeletal and membrane networks. , 2009, Biochemical Society transactions.

[36]  Anne-Kristin Kaster,et al.  Methanogenic archaea: ecologically relevant differences in energy conservation , 2008, Nature Reviews Microbiology.

[37]  W. Whitman,et al.  Metabolic, Phylogenetic, and Ecological Diversity of the Methanogenic Archaea , 2008, Annals of the New York Academy of Sciences.

[38]  Hailiang Dong,et al.  Microbial response to salinity change in Lake Chaka, a hypersaline lake on Tibetan plateau. , 2007, Environmental microbiology.

[39]  J. Hackstein,et al.  The competitive success of Methanomicrococcus blatticola, a dominant methylotrophic methanogen in the cockroach hindgut, is supported by high substrate affinities and favorable thermodynamics. , 2007, FEMS microbiology ecology.

[40]  R. Cavicchioli.  Archaea Molecular and Cellular Biology , 2007 .

[41]  W. F. Fricke,et al.  The Genome Sequence of Methanosphaera stadtmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H2 for Methane Formation and ATP Synthesis , 2006, Journal of bacteriology.

[42]  Johannes Söding,et al.  The HHpred interactive server for protein homology detection and structure prediction , 2005, Nucleic Acids Res..

[43]  C. Plugge.  Anoxic media design, preparation, and considerations. , 2005, Methods in enzymology.

[44]  J. Hackstein,et al.  The energy metabolism of Methanomicrococcus blatticola: physiological and biochemical aspects , 2005, Antonie van Leeuwenhoek.

[45]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[46]  T. Miller,et al.  Methanosphaera stadtmaniae gen. nov., sp. nov.: a species that forms methane by reducing methanol with hydrogen , 1985, Archives of Microbiology.

[47]  N. Pfennig,et al.  Über das Vitamin B12-Bedürfnis phototropher Schwefelbakterien , 1966, Archiv für Mikrobiologie.

[48]  E. Delong,et al.  Identification of Methyl Coenzyme M Reductase A (mcrA) Genes Associated with Methane-Oxidizing Archaea , 2003, Applied and Environmental Microbiology.

[49]  Robert Huber,et al.  Prokaryotic phylogenetic diversity and corresponding geochemical data of the brine-seawater interface of the Shaban Deep, Red Sea. , 2002, Environmental microbiology.

[50]  M. Borodovsky,et al.  GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. , 2001, Nucleic acids research.

[51]  J. Hackstein,et al.  Methanomicrococcus blatticola gen. nov., sp. nov., a methanol- and methylamine-reducing methanogen from the hindgut of the cockroach Periplaneta americana. , 2000, International journal of systematic and evolutionary microbiology.

[52]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[53]  M. Roberts,et al.  Osmoadaptation in Archaea , 1999, Applied and Environmental Microbiology.

[54]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[55]  Huaiyu Zhu.  On Information and Sufficiency , 1997 .

[56]  D. Hochstrasser,et al.  The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences , 1993, Electrophoresis.

[57]  J. Menaia.  Osmotics of halophilic methanogenic archaeobacteria , 1992 .

[58]  E. Rosenberg,et al.  Microbial mats : physiological ecology of benthic microbial communities , 1989 .

[59]  M. Ginzburg,et al.  Ion Metabolism in a Halobacterium : I. Influence of age of culture on intracellular concentrations , 1970 .

[60]  J. Gower.  Some distance properties of latent root and vector methods used in multivariate analysis , 1966 .

[61]  E. Parzen.  On Estimation of a Probability Density Function and Mode , 1962 .

[62]  Joseph L. Zinnes,et al.  Theory and Methods of Scaling. , 1958 .