Bowen JL, Ward BB, Morrison HG, Hobbie JE, Valiela I, Deegan LA, Sogin ML: Microbial community composition in sediments resists perturbation by nutrient enrichment. ISME J. 2011, 5: 1540-1548. 10.1038/ismej.2011.22.
Article
PubMed Central
PubMed
Google Scholar
Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, VerBerkmoes NC, Wilkins MJ, Hettich RL, Lipton MS, Williams KH, Long PE, Banfield JF: Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science. 2012, 337: 1661-1665. 10.1126/science.1224041.
Article
CAS
PubMed
Google Scholar
Jorgensen SL, Hannisdal B, Lanzén A, Baumberger T, Flesland K, Fonseca R, Ovreås L, Steen IH, Thorseth IH, Pedersen RB, Schleper C: Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge. Proc Natl Acad Sci U S A. 2012, 109: E2846-E2855. 10.1073/pnas.1207574109.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hamdan LJ, Coffin RB, Sikaroodi M, Greinert J, Treude T, Gillevet PM: Ocean currents shape the microbiome of Arctic marine sediments. ISME J. 2012, 7: 685-696.
Article
PubMed Central
PubMed
Google Scholar
Wang Y, Sheng H-F, He Y, Wu J-Y, Jiang Y-X, Tam NF-Y, Zhou H-W: Comparison of the levels of bacterial diversity in freshwater, intertidal wetland, and marine sediments by using millions of illumina tags. Appl Environ Microbiol. 2012, 78: 8264-8271. 10.1128/AEM.01821-12.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tang S, Gong Y, Edwards EA: Semi-automatic in silico gap closure enabled de novo assembly of two Dehalobacter genomes from metagenomic data. PLoS One. 2012, 7: e52038-10.1371/journal.pone.0052038.
Article
PubMed Central
CAS
PubMed
Google Scholar
Iverson V, Morris RM, Frazar CD, Berthiaume CT, Morales RL, Armbrust EV: Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science. 2012, 335: 587-590. 10.1126/science.1212665.
Article
CAS
PubMed
Google Scholar
Blazejak A, Schippers A: High abundance of JS-1- and Chloroflexi-related Bacteria in deeply buried marine sediments revealed by quantitative, real-time PCR. FEMS Microbiol Ecol. 2010, 72: 198-207. 10.1111/j.1574-6941.2010.00838.x.
Article
CAS
PubMed
Google Scholar
Kirk Harris J, Gregory Caporaso J, Walker JJ, Spear JR, Gold NJ, Robertson CE, Hugenholtz P, Goodrich J, McDonald D, Knights D, Marshall P, Tufo H, Knight R, Pace NR: Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. ISME J. 2012, 7: 50-60.
Article
PubMed Central
PubMed
Google Scholar
Kadnikov VV, Mardanov AV, Beletsky AV, Shubenkova OV, Pogodaeva TV, Zemskaya TI, Ravin NV, Skryabin KG: Microbial community structure in methane hydrate-bearing sediments of freshwater Lake Baikal. FEMS Microbiol Ecol. 2012, 79: 348-358. 10.1111/j.1574-6941.2011.01221.x.
Article
CAS
PubMed
Google Scholar
Ikenaga M, Guevara R, Dean AL, Pisani C, Boyer JN: Changes in community structure of sediment bacteria along the Florida coastal everglades marsh-mangrove-seagrass salinity gradient. Microb Ecol. 2010, 59: 284-295. 10.1007/s00248-009-9572-2.
Article
PubMed
Google Scholar
Kube M, Beck A, Zinder SH, Kuhl H, Reinhardt R, Adrian L: Genome sequence of the chlorinated compound-respiring bacterium Dehalococcoides species strain CBDB1. Nat Biotechnol. 2005, 23: 1269-1273. 10.1038/nbt1131.
Article
CAS
PubMed
Google Scholar
McMurdie PJ, Behrens SF, Müller JA, Göke J, Ritalahti KM, Wagner R, Goltsman E, Lapidus A, Holmes S, Löffler FE, Spormann AM: Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. PLoS Genet. 2009, 5: e1000714-10.1371/journal.pgen.1000714.
Article
PubMed Central
PubMed
Google Scholar
Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, Deboy RT, Khouri HM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Nelson KE, Kang KH, Impraim M, Tran K, Robinson JM, Forberger HA, Fraser CM, Zinder SH, Heidelberg JF: Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science. 2005, 307: 105-108. 10.1126/science.1102226.
Article
CAS
PubMed
Google Scholar
Löffler FE, Yan J, Ritalahti KM, Adrian L, Edwards EA, Konstantinidis KT, Müller JA, Fullerton H, Zinder SH, Spormann AM: Dehalococcoides mccartyi gen. nov., sp. nov., obligate organohalide-respiring anaerobic bacteria, relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidetes classis nov., within the phylum Chloroflexi. Int J Syst Evol Microbiol. 2012, 63: 625-635.
Article
PubMed
Google Scholar
Chang Y-J, Land M, Hauser L, Chertkov O, Del Rio TG, Nolan M, Copeland A, Tice H, Cheng J-F, Lucas S, Han C, Goodwin L, Pitluck S, Ivanova N, Ovchinikova G, Pati A, Chen A, Palaniappan K, Mavromatis K, Liolios K, Brettin T, Fiebig A, Rohde M, Abt B, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, et al: Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21). Stand Genomic Sci. 2011, 5: 97-111. 10.4056/sigs.2114901.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tang K-H, Barry K, Chertkov O, Dalin E, Han CS, Hauser LJ, Honchak BM, Karbach LE, Land ML, Lapidus A, Larimer FW, Mikhailova N, Pitluck S, Pierson BK, Blankenship RE: Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus. BMC Genomics. 2011, 12: 334-10.1186/1471-2164-12-334.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yamada T, Sekiguchi Y, Hanada S, Imachi H, Ohashi A, Harada H, Kamagata Y: Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. Int J Syst Evol Microbiol. 2006, 56: 1331-1340. 10.1099/ijs.0.64169-0.
Article
CAS
PubMed
Google Scholar
Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb F, Colman A, Tallon LJ, Badger JH, Madupu R, Ward NL, Eisen JA: Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS One. 2009, 4: e4207-10.1371/journal.pone.0004207.
Article
PubMed Central
PubMed
Google Scholar
Handley KM, Wrighton KC, Piceno YM, Andersen GL, Desantis TZ, Williams KH, Wilkins MJ, N’guessan AL, Peacock A, Bargar J, Long PE, Banfield JF: High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment. FEMS Microbiol Ecol. 2012, 81: 188-204. 10.1111/j.1574-6941.2012.01363.x.
Article
CAS
PubMed
Google Scholar
Williams KH, Long PE, Davis JA, Wilkins MJ, N’Guessan AL, Steefel CI, Yang L, Newcomer D, Spane FA, Kerkhof LJ, McGuinness L, Dayvault R, Lovley DR: Acetate availability and its influence on sustainable bioremediation of Uranium-contaminated groundwater. Geomicrobiol J. 2011, 28: 519-539. 10.1080/01490451.2010.520074.
Article
CAS
Google Scholar
Campbell KM, Veeramani H, Ulrich K-U, Blue LY, Giammar DE, Bernier-Latmani R, Stubbs JE, Suvorova E, Yabusaki S, Lezama-Pacheco JS, Mehta A, Long PE, Bargar JR: Oxidative dissolution of biogenic Uraninite in groundwater at Old Rifle, CO. Environ Sci Tech. 2011, 45: 8748-8754. 10.1021/es200482f.
Article
CAS
Google Scholar
Peng Y, Leung HCM, Yiu SM, Chin FYL: IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012, 28: 1420-1428. 10.1093/bioinformatics/bts174.
Article
CAS
PubMed
Google Scholar
Dick GJ, Andersson AF, Baker BJ, Simmons SL, Thomas BC, Yelton AP, Banfield JF: Community-wide analysis of microbial genome sequence signatures. Genome Biol. 2009, 10: R85-10.1186/gb-2009-10-8-r85.
Article
PubMed Central
PubMed
Google Scholar
Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ: Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinforma. 2010, 11: 119-10.1186/1471-2105-11-119.
Article
Google Scholar
Zerbino DR, Birney E: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008, 18: 821-829. 10.1101/gr.074492.107.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sorek R, Zhu Y, Creevey CJ, Francino MP, Bork P, Rubin EM: Genome-wide experimental determination of barriers to horizontal gene transfer. Science. 2007, 318: 1449-1452. 10.1126/science.1147112.
Article
CAS
PubMed
Google Scholar
Wu M, Eisen JA: A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 2008, 9: R151-10.1186/gb-2008-9-10-r151.
Article
PubMed Central
PubMed
Google Scholar
Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH: UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics. 2007, 23: 1282-1288. 10.1093/bioinformatics/btm098.
Article
CAS
PubMed
Google Scholar
Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 1999, 27: 29-34. 10.1093/nar/27.1.29.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M: KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012, 40: 109-114.
Article
Google Scholar
Mulder N, Apweiler R: InterPro and InterProScan: tools for protein sequence classification and comparison. Methods Mol Biol. 2007, 396: 59-70. 10.1007/978-1-59745-515-2_5.
Article
CAS
PubMed
Google Scholar
Schattner P, Brooks AN, Lowe TM: The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 2005, 33: 686-689. 10.1093/nar/gki366.
Article
Google Scholar
Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32: 1792-1797. 10.1093/nar/gkh340.
Article
PubMed Central
CAS
PubMed
Google Scholar
Edgar RC: MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinforma. 2004, 5: 113-10.1186/1471-2105-5-113.
Article
Google Scholar
Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003, 52: 696-704. 10.1080/10635150390235520.
Article
PubMed
Google Scholar
Abascal F, Zardoya R, Posada D: ProtTest: selection of best-fit models of protein evolution. Bioinformatics. 2005, 21: 2104-2105. 10.1093/bioinformatics/bti263.
Article
CAS
PubMed
Google Scholar
Darriba D, Taboada GL, Doallo R, Posada D: ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics. 2011, 27: 1164-1165. 10.1093/bioinformatics/btr088.
Article
CAS
PubMed
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410.
Article
CAS
PubMed
Google Scholar
Huson DH, Auch AF, Qi J, Schuster SC: MEGAN analysis of metagenomic data. Genome Res. 2007, 17: 377-386. 10.1101/gr.5969107.
Article
PubMed Central
CAS
PubMed
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10: R25-10.1186/gb-2009-10-3-r25.
Article
PubMed Central
PubMed
Google Scholar
Gutell RR, Larsen N, Woese CR: Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev. 1994, 58: 10-26.
PubMed Central
CAS
PubMed
Google Scholar
Jones AL: The future of taxonomy. Adv Appl Microbiol. 2012, 80: 23-35.
Article
CAS
PubMed
Google Scholar
Teeling H, Glöckner FO: Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective. Brief Bioinform. 2012, 13: 728-742. 10.1093/bib/bbs039.
Article
PubMed Central
PubMed
Google Scholar
Miller CS, Baker BJ, Thomas BC, Singer SW, Banfield JF: EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biol. 2011, 12: R44-10.1186/gb-2011-12-5-r44.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yabe S, Aiba Y, Sakai Y, Hazaka M, Yokota A: Thermosporothrix hazakensis gen. nov., sp. nov., isolated from compost, description of Thermosporotrichaceae fam. nov. within the class Ktedonobacteria Cavaletti et al. 2007 and emended description of the class Ktedonobacteria. Int J Syst Evol Microbiol. 2010, 60: 1794-1801. 10.1099/ijs.0.018069-0.
Article
CAS
PubMed
Google Scholar
Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA: Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. PLoS One. 2011, 6: e18011-10.1371/journal.pone.0018011.
Article
PubMed Central
CAS
PubMed
Google Scholar
Stark M, Berger SA, Stamatakis A, Von Mering C: MLTreeMap–accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies. BMC Genomics. 2010, 11: 461-10.1186/1471-2164-11-461.
Article
PubMed Central
PubMed
Google Scholar
Bendtsen JD, Nielsen H, Von Heijne G, Brunak S: Improved prediction of signal peptides: SignalP 3.0. J Mol Biol. 2004, 340: 783-795. 10.1016/j.jmb.2004.05.028.
Article
PubMed
Google Scholar
Petersen TN, Brunak S, Von Heijne G, Nielsen H: SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011, 8: 785-786. 10.1038/nmeth.1701.
Article
CAS
PubMed
Google Scholar
Bendtsen JD, Nielsen H, Widdick D, Palmer T, Brunak S: Prediction of twin-arginine signal peptides. BMC Bioinforma. 2005, 6: 167-10.1186/1471-2105-6-167.
Article
Google Scholar
Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO: SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007, 35: 7188-7196. 10.1093/nar/gkm864.
Article
PubMed Central
CAS
PubMed
Google Scholar
Giovannoni SJ, Rappé MS, Vergin KL, Adair NL: 16S rRNA genes reveal stratified open ocean bacterioplankton populations related to the Green Non-Sulfur bacteria. Proc Natl Acad Sci U S A. 1996, 93: 7979-7984. 10.1073/pnas.93.15.7979.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chandler D, Brockman F, Bailey T, Fredrickson J: Phylogenetic diversity of Archaea and Bacteria in a deep subsurface Paleosol. Microb Ecol. 1998, 36: 37-50. 10.1007/s002489900091.
Article
CAS
PubMed
Google Scholar
Alfreider A, Vogt C, Babel W: Microbial diversity in an in situ reactor system treating monochlorobenzene contaminated groundwater as revealed by 16S ribosomal DNA analysis. Syst Appl Microbiol. 2002, 25: 232-240. 10.1078/0723-2020-00111.
Article
CAS
PubMed
Google Scholar
Jiang L, Zheng Y, Peng X, Zhou H, Zhang C, Xiao X, Wang F: Vertical distribution and diversity of sulfate-reducing prokaryotes in the Pearl River estuarine sediments, Southern China. FEMS Microbiol Ecol. 2009, 70: 93-106.
Article
PubMed
Google Scholar
Ley RE, Harris JK, Wilcox J, Spear JR, Miller SR, Bebout BM, Maresca JA, Bryant DA, Sogin ML, Pace NR: Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl Environ Microbiol. 2006, 72: 3685-3695. 10.1128/AEM.72.5.3685-3695.2006.
Article
PubMed Central
CAS
PubMed
Google Scholar
Inagaki F, Nunoura T, Nakagawa S, Teske A, Lever M, Lauer A, Suzuki M, Takai K, Delwiche M, Colwell FS, Nealson KH, Horikoshi K, D’Hondt S, Jørgensen BB: Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proc Natl Acad Sci U S A. 2006, 103: 2815-2820. 10.1073/pnas.0511033103.
Article
PubMed Central
CAS
PubMed
Google Scholar
Takeuchi M, Komai T, Hanada S, Tamaki H, Tanabe S, Miyachi Y, Uchiyama M, Nakazawa T, Kimura K, Kamagata Y: Bacterial and archaeal 16S rRNA genes in late Pleistocene to Holocene muddy sediments from the Kanto Plain of Japan. Geomicrobiol J. 2009, 26: 104-118. 10.1080/01490450802662355.
Article
CAS
Google Scholar
Harrison BK, Zhang H, Berelson W, Orphan VJ: Variations in archaeal and bacterial diversity associated with the sulfate-methane transition zone in continental margin sediments (Santa Barbara Basin, California). Appl Environ Microbiol. 2009, 75: 1487-1499. 10.1128/AEM.01812-08.
Article
PubMed Central
CAS
PubMed
Google Scholar
Teske A, Durbin A, Ziervogel K, Cox C, Arnosti C: Microbial community composition and function in permanently cold seawater and sediments from an arctic fjord of svalbard. Appl Environ Microbiol. 2011, 77: 2008-2018. 10.1128/AEM.01507-10.
Article
PubMed Central
CAS
PubMed
Google Scholar
Siddaramappa S, Challacombe JF, Delano SF, Green LD, Daligault H, Bruce D, Detter C, Tapia R, Han S, Goodwin L, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Land M, Chang Y-J, Kyrpides NC, Ovchinnikova G, Hauser L, Lapidus A, Yan J, Bowman KS, Da Costa MS, Rainey FA, Moe WM: Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9 T ) and comparison to “Dehalococcoides” strains. Stand Genomic Sci. 2012, 6: 251-264. 10.4056/sigs.2806097.
Article
PubMed Central
PubMed
Google Scholar
Ahsanul Islam M, Edwards EA, Mahadevan R: Characterizing the metabolism of Dehalococcoides with a constraint-based model. PLoS Comput Biol. 2010, 6: e1000887-10.1371/journal.pcbi.1000887.
Article
PubMed Central
PubMed
Google Scholar
Moparthi VK, Hägerhäll C: The evolution of respiratory chain complex I from a smaller last common ancestor consisting of 11 protein subunits. J Mol Evol. 2011, 72: 484-497. 10.1007/s00239-011-9447-2.
Article
PubMed Central
CAS
PubMed
Google Scholar
Marco-Urrea E, Paul S, Khodaverdi V, Seifert J, Von Bergen M, Kretzschmar U, Adrian L: Identification and characterization of a re-citrate synthase in Dehalococcoides strain CBDB1. J Bacteriol. 2011, 193: 5171-5178. 10.1128/JB.05120-11.
Article
PubMed Central
CAS
PubMed
Google Scholar
Diesterhaft MD, Freese E: Role of pyruvate carboxylase, phosphoenolpyruvate carboxykinase, and malic enzyme during growth and sporulation of Bacillus subtilis. J Biol Chem. 1973, 248: 6062-6070.
CAS
PubMed
Google Scholar
Messerschmidt A, Niessen H, Abt D, Einsle O, Schink B, Kroneck PMH: Crystal structure of pyrogallol-phloroglucinol transhydroxylase, an Mo enzyme capable of intermolecular hydroxyl transfer between phenols. Proc Natl Acad Sci U S A. 2004, 101: 11571-11576. 10.1073/pnas.0404378101.
Article
PubMed Central
CAS
PubMed
Google Scholar
Brune A, Schink B: Pyrogallol-to-phloroglucinol conversion and other hydroxyl-transfer reactions catalyzed by cell extracts of Pelobacter acidigallici. J Bacteriol. 1990, 172: 1070-1076.
PubMed Central
CAS
PubMed
Google Scholar
Brune A, Schnell S, Schink B: Sequential transhydroxylations converting hydroxyhydroquinone to phloroglucinol in the strictly anaerobic, fermentative bacterium Pelobacter massiliensis. Appl Environ Microbiol. 1992, 58: 1861-1868.
PubMed Central
CAS
PubMed
Google Scholar
Mai X, Adams MW: Characterization of a fourth type of 2-keto acid-oxidizing enzyme from a hyperthermophilic archaeon: 2-ketoglutarate ferredoxin oxidoreductase from Thermococcus litoralis. J Bacteriol. 1996, 178: 5890-5896.
PubMed Central
CAS
PubMed
Google Scholar
Zhang Q, Iwasaki T, Wakagi T, Oshima T: 2-oxoacid:ferredoxin oxidoreductase from the thermoacidophilic archaeon, Sulfolobus sp. strain 7. J Biochem. 1996, 120: 587-599. 10.1093/oxfordjournals.jbchem.a021454.
Article
CAS
PubMed
Google Scholar
Fukuda E, Wakagi T: Substrate recognition by 2-oxoacid:ferredoxin oxidoreductase from Sulfolobus sp. strain 7. Biochim Biophys Acta. 2002, 1597: 74-80. 10.1016/S0167-4838(02)00280-7.
Article
CAS
PubMed
Google Scholar
Ma K, Hutchins A, Sung SJ, Adams MW: Pyruvate ferredoxin oxidoreductase from the hyperthermophilic archaeon, Pyrococcus furiosus, functions as a CoA-dependent pyruvate decarboxylase. Proc Natl Acad Sci U S A. 1997, 94: 9608-9613. 10.1073/pnas.94.18.9608.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ragsdale SW, Pierce E: Acetogenesis and the Wood-Ljungdahl pathway of CO(2) fixation. Biochim Biophys Acta. 2008, 1784: 1873-1898. 10.1016/j.bbapap.2008.08.012.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mai X, Adams MW: Purification and characterization of two reversible and ADP-dependent acetyl coenzyme A synthetases from the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol. 1996, 178: 5897-5903.
PubMed Central
CAS
PubMed
Google Scholar
Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer SW, Eisen JA, Banfield JF: Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun. 2013, In press
Google Scholar
Vignais PM: Hydrogenases and H(+)-reduction in primary energy conservation. Results Probl Cell Differ. 2008, 45: 223-252. 10.1007/400_2006_027.
Article
CAS
PubMed
Google Scholar
Rosier C, Leys N, Henoumont C, Mergeay M, Wattiez R: Purification and characterization of the acetone carboxylase of Cupriavidus metallidurans strain CH34. Appl Environ Microbiol. 2012, 78: 4516-4518. 10.1128/AEM.07974-11.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yamada T, Sekiguchi Y, Imachi H, Kamagata Y, Ohashi A, Harada H: Diversity, localization, and physiological properties of filamentous microbes belonging to Chloroflexi subphylum I in mesophilic and thermophilic methanogenic sludge granules. Appl Environ Microbiol. 2005, 71: 7493-7503. 10.1128/AEM.71.11.7493-7503.2005.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sekiguchi Y: Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level. Int J Syst Evol Micr. 2003, 53: 1843-1851. 10.1099/ijs.0.02699-0.
Article
CAS
Google Scholar
Lin X, Kennedy D, Fredrickson J, Bjornstad B, Konopka A: Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site. Environ Microbiol. 2012, 14: 414-425. 10.1111/j.1462-2920.2011.02659.x.
Article
CAS
PubMed
Google Scholar
Singer E, Heidelberg JF, Dhillon A, Edwards KJ: Metagenomic insights into the dominant Fe(II) oxidizing Zetaproteobacteria from an iron mat at Lō´ihi, Hawai´l. Front Microbiol. 2013, 4: 52-
Article
PubMed Central
PubMed
Google Scholar
Hinsley AP, Berks BC: Specificity of respiratory pathways involved in the reduction of sulfur compounds by Salmonella enterica. Microbiology. 2002, 148: 3631-3638.
Article
CAS
PubMed
Google Scholar
Ralebits TK, Senior E, Van Verseveld HW: Microbial aspects of atrazine degradation in natural environments. Biodegradation. 2002, 13: 11-19. 10.1023/A:1016329628618.
Article
PubMed
Google Scholar
Kindaichi T, Yuri S, Ozaki N, Ohashi A: Ecophysiological role and function of uncultured Chloroflexi in an anammox reactor. Water Sci Technol. 2012, 66: 2556-2561. 10.2166/wst.2012.479.
Article
CAS
PubMed
Google Scholar
Sutcliffe IC: Cell envelope architecture in the Chloroflexi: a shifting frontline in a phylogenetic turf war. Environ Microbiol. 2011, 13: 279-282. 10.1111/j.1462-2920.2010.02339.x.
Article
PubMed
Google Scholar
White DC, Geyer R, Peacock AD, Hedrick DB, Koenigsberg SS, Sung Y, He J, Löffler FE: Phospholipid furan fatty acids and ubiquinone-8: lipid biomarkers that may protect Dehalococcoides strains from free radicals. Appl Environ Microbiol. 2005, 71: 8426-8433. 10.1128/AEM.71.12.8426-8433.2005.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sorokin DY, Lücker S, Vejmelkova D, Kostrikina NA, Kleerebezem R, Rijpstra WIC, Damsté JSS, Le Paslier D, Muyzer G, Wagner M, Van Loosdrecht MCM, Daims H: Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi. ISME J. 2012, 6: 2245-2256. 10.1038/ismej.2012.70.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pati A, Labutti K, Pukall R, Nolan M, Glavina Del Rio T, Tice H, Cheng J-F, Lucas S, Chen F, Copeland A, Ivanova N, Mavromatis K, Mikhailova N, Pitluck S, Bruce D, Goodwin L, Land M, Hauser L, Chang Y-J, Jeffries CD, Chen A, Palaniappan K, Chain P, Brettin T, Sikorski J, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, et al: Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022). Stand Genomic Sci. 2010, 2: 49-56. 10.4056/sigs.601105.
Article
PubMed Central
PubMed
Google Scholar
Kiss H, Cleland D, Lapidus A, Lucas S, Del Rio TG, Nolan M, Tice H, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang Y-J, Jeffries CD, Lu M, Brettin T, Detter JC, Göker M, Tindall BJ, Beck B, McDermott TR, Woyke T, Bristow J, et al: Complete genome sequence of “Thermobaculum terrenum” type strain (YNP1). Stand Genomic Sci. 2010, 3: 153-162. 10.4056/sigs.1153107.
Article
PubMed Central
PubMed
Google Scholar
Kiss H, Nett M, Domin N, Martin K, Maresca JA, Copeland A, Lapidus A, Lucas S, Berry KW, Glavina Del Rio T, Dalin E, Tice H, Pitluck S, Richardson P, Bruce D, Goodwin L, Han C, Detter JC, Schmutz J, Brettin T, Land M, Hauser L, Kyrpides NC, Ivanova N, Göker M, Woyke T, Klenk H-P, Bryant DA: Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95(T)). Stand Genomic Sci. 2011, 5: 356-370. 10.4056/sigs.2194987.
Article
PubMed Central
CAS
PubMed
Google Scholar
Jarrell KF, McBride MJ: The surprisingly diverse ways that prokaryotes move. Nat Rev Microbiol. 2008, 6: 466-476. 10.1038/nrmicro1900.
Article
CAS
PubMed
Google Scholar
Krasotkina J, Walters T, Maruya KA, Ragsdale SW: Characterization of the B12- and iron-sulfur-containing reductive dehalogenase from Desulfitobacterium chlororespirans. J Biol Chem. 2001, 276: 40991-40997. 10.1074/jbc.M106217200.
Article
CAS
PubMed
Google Scholar
Ni S, Fredrickson JK, Xun L: Purification and characterization of a novel 3-chlorobenzoate-reductive dehalogenase from the cytoplasmic membrane of Desulfomonile tiedjei DCB-1. J Bacteriol. 1995, 177: 5135-5139.
PubMed Central
CAS
PubMed
Google Scholar
Adrian L, Rahnenführer J, Gobom J, Hölscher T: Identification of a chlorobenzene reductive dehalogenase in Dehalococcoides sp. strain CBDB1. Appl Environ Microbiol. 2007, 73: 7717-7724. 10.1128/AEM.01649-07.
Article
PubMed Central
CAS
PubMed
Google Scholar
Van de Pas BA, Gerritse J, De Vos WM, Schraa G, Stams AJ: Two distinct enzyme systems are responsible for tetrachloroethene and chlorophenol reductive dehalogenation in Desulfitobacterium strain PCE1. Arch Microbiol. 2001, 176: 165-169. 10.1007/s002030100316.
Article
CAS
PubMed
Google Scholar
Hesseler M, Bogdanović X, Hidalgo A, Berenguer J, Palm GJ, Hinrichs W, Bornscheuer UT: Cloning, functional expression, biochemical characterization, and structural analysis of a haloalkane dehalogenase from Plesiocystis pacifica SIR-1. Appl Microbiol Biotechnol. 2011, 91: 1049-1060. 10.1007/s00253-011-3328-x.
Article
CAS
PubMed
Google Scholar
Chan WY, Wong M, Guthrie J, Savchenko AV, Yakunin AF, Pai EF, Edwards EA: Sequence- and activity-based screening of microbial genomes for novel dehalogenases. Microb Biotechnol. 2010, 3: 107-120. 10.1111/j.1751-7915.2009.00155.x.
Article
PubMed Central
CAS
PubMed
Google Scholar
Smidt H, De Vos WM: Anaerobic microbial dehalogenation. Annu Rev Microbiol. 2004, 58: 43-73. 10.1146/annurev.micro.58.030603.123600.
Article
CAS
PubMed
Google Scholar
Krzmarzick MJ, Crary BB, Harding JJ, Oyerinde OO, Leri AC, Myneni SCB, Novak PJ: Natural niche for organohalide-respiring Chloroflexi. Appl Environ Microbiol. 2012, 78: 393-401. 10.1128/AEM.06510-11.
Article
PubMed Central
CAS
PubMed
Google Scholar