title: Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass.
abstract: Thermophilic bacteria are a potential source of enzymes for the deconstruction of lignocellulosic biomass. However, the complement of proteins used to deconstruct biomass and the specific roles of different microbial groups in thermophilic biomass deconstruction are not well-explored. Here we report on the metagenomic and proteogenomic analyses of a compost-derived bacterial consortium adapted to switchgrass at elevated temperature with high levels of glycoside hydrolase activities. Near-complete genomes were reconstructed for the most abundant populations, which included composite genomes for populations closely related to sequenced strains of Thermus thermophilus and Rhodothermus marinus, and for novel populations that are related to thermophilic Paenibacilli and an uncultivated subdivision of the little-studied Gemmatimonadetes phylum. Partial genomes were also reconstructed for a number of lower abundance thermophilic Chloroflexi populations. Identification of genes for lignocellulose processing and metabolic reconstructions suggested Rhodothermus, Paenibacillus and Gemmatimonadetes as key groups for deconstructing biomass, and Thermus as a group that may primarily metabolize low molecular weight compounds. Mass spectrometry-based proteomic analysis of the consortium was used to identify >3000 proteins in fractionated samples from the cultures, and confirmed the importance of Paenibacillus and Gemmatimonadetes to biomass deconstruction. These studies also indicate that there are unexplored proteins with important roles in bacterial lignocellulose deconstruction.
authors.affiliation: Joint BioEnergy Institute, Emeryville, California, United States of America. patrikd@llnl.gov
authors.forename: Patrik
authors.initials: P
authors.lastname: D'haeseleer
authors.forename: John M
authors.initials: JM
authors.lastname: Gladden
authors.forename: Martin
authors.initials: M
authors.lastname: Allgaier
authors.forename: Patrik S G
authors.initials: PS
authors.lastname: Chain
authors.forename: Susannah G
authors.initials: SG
authors.lastname: Tringe
authors.forename: Stephanie A
authors.initials: SA
authors.lastname: Malfatti
authors.forename: Joshua T
authors.initials: JT
authors.lastname: Aldrich
authors.forename: Carrie D
authors.initials: CD
authors.lastname: Nicora
authors.forename: Errol W
authors.initials: EW
authors.lastname: Robinson
authors.forename: Ljiljana
authors.initials: L
authors.lastname: Paša-Tolić
authors.forename: Philip
authors.initials: P
authors.lastname: Hugenholtz
authors.forename: Blake A
authors.initials: BA
authors.lastname: Simmons
authors.forename: Steven W
authors.initials: SW
authors.lastname: Singer
mesh_terms: D000220:Adaptation, Biological; D001419:Bacteria / Q000235:genetics* / Q000378:metabolism*; D001482:Base Composition; D018533:Biomass; D050260:Carbohydrate Metabolism; D023281:Genomics; D008031:Lignin / Q000378:metabolism; D055432:Metabolomics; D056186:Metagenomics; D058977:Molecular Sequence Annotation; D008897:Panicum / Q000382:microbiology*; D010802:Phylogeny; D040901:Proteomics; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; C036909:lignocellulose; D008031:Lignin
references.citation: PLoS One. 2013;8(1):e53779
references.pmid: 23341999
references.citation: Stand Genomic Sci. 2011 Nov 30;5(2):248-53
references.pmid: 22180827
references.citation: J Bacteriol. 2005 Sep;187(18):6258-64
references.pmid: 16159757
references.citation: Microbiol Mol Biol Rev. 2008 Dec;72(4):557-78, Table of Contents
references.pmid: 19052320
references.citation: Biotechnol Bioeng. 2012 May;109(5):1140-5
references.pmid: 22125273
references.citation: Biotechnol Lett. 2010 Oct;32(10):1351-9
references.pmid: 20495950
references.citation: Nucleic Acids Res. 2012 Jul;40(Web Server issue):W445-51
references.pmid: 22645317
references.citation: Bioresour Technol. 2010 Dec;101(23):9097-105
references.pmid: 20678930
references.citation: Bioinformatics. 2008 Jul 1;24(13):1556-8
references.pmid: 18453552
references.citation: J Proteome Res. 2005 Nov-Dec;4(6):2397-403
references.pmid: 16335993
references.citation: Anal Chem. 2006 Nov 15;78(22):7796-801
references.pmid: 17105173
references.citation: Anal Chem. 2012 Mar 20;84(6):2862-7
references.pmid: 22339560
references.citation: Appl Environ Microbiol. 1994 Dec;60(12):4495-9
references.pmid: 16349464
references.citation: Genome Biol. 2008;9(12):242
references.pmid: 19133109
references.citation: Stand Genomic Sci. 2010 Jan 28;2(1):49-56
references.pmid: 21304677
references.citation: PLoS Genet. 2010 Sep 23;6(9):e1001129
references.pmid: 20885794
references.citation: Science. 2011 Jan 28;331(6016):463-7
references.pmid: 21273488
references.citation: Appl Microbiol Biotechnol. 2006 Aug;71(6):942-52
references.pmid: 16395545
references.citation: Science. 2005 Jun 24;308(5730):1915-20
references.pmid: 15879173
references.citation: Appl Microbiol Biotechnol. 2008 Sep;80(3):381-8
references.pmid: 18636256
references.citation: PLoS One. 2010 Jan 21;5(1):e8812
references.pmid: 20098679
references.citation: Bioresour Technol. 2010 Jul;101(13):4900-6
references.pmid: 19945861
references.citation: PLoS One. 2009;4(4):e5271
references.pmid: 19384422
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D123-9
references.pmid: 22086953
references.citation: Stand Genomic Sci. 2010 Oct 27;3(2):153-62
references.pmid: 21304745
references.citation: Biosci Biotechnol Biochem. 2007 Jan;71(1):1-15
references.pmid: 17213657
references.citation: BMC Genomics. 2011 Nov 24;12:577
references.pmid: 22115438
references.citation: Microbiol Mol Biol Rev. 2002 Sep;66(3):506-77, table of contents
references.pmid: 12209002
references.citation: Appl Biochem Biotechnol. 2010 May;161(1-8):147-56
references.pmid: 19790003
references.citation: J Proteome Res. 2011 Dec 2;10(12):5302-14
references.pmid: 21988591
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D233-8
references.pmid: 18838391
references.citation: Nat Rev Microbiol. 2009 Mar;7(3):196-205
references.pmid: 19219053
references.citation: J Proteome Res. 2006 Nov;5(11):3008-17
references.pmid: 17081052
references.citation: J Bacteriol. 2010 Oct;192(20):5499-505
references.pmid: 20729360
references.citation: Bioinformatics. 2009 Aug 15;25(16):2028-34
references.pmid: 19535538
references.citation: BMC Biotechnol. 2012 Jul 03;12:38
references.pmid: 22759983
references.citation: PLoS Comput Biol. 2012;8(10):e1002743
references.pmid: 23133348
references.citation: PLoS One. 2012;7(5):e36740
references.pmid: 22629327
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D742-53
references.pmid: 22102576
references.citation: Genome Biol. 2010;11(10):R106
references.pmid: 20979621
references.citation: Nature. 2007 Nov 22;450(7169):560-5
references.pmid: 18033299
references.citation: Nat Biotechnol. 2004 May;22(5):547-53
references.pmid: 15064768
references.citation: Appl Environ Microbiol. 2006 Mar;72(3):1719-28
references.pmid: 16517615
references.citation: Enzyme Microb Technol. 2000 Sep 1;27(6):414-422
references.pmid: 10938421
references.citation: Appl Environ Microbiol. 2011 Sep;77(17):6295-300
references.pmid: 21764958
references.citation: Stand Genomic Sci. 2009 Jul 20;1(1):63-7
references.pmid: 21304638
references.citation: Int J Syst Evol Microbiol. 2003 Jul;53(Pt 4):1155-1163
references.pmid: 12892144
references.citation: Stand Genomic Sci. 2009 Dec 29;1(3):283-90
references.pmid: 21304669
references.citation: Curr Opin Biotechnol. 2011 Jun;22(3):394-400
references.pmid: 21071202
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D115-22
references.pmid: 22194640
references.citation: Biotechnol Biofuels. 2012 Apr 10;5(1):20
references.pmid: 22490508
references.citation: Nature. 2009 Dec 24;462(7276):1056-60
references.pmid: 20033048
references.citation: Microbiol Rev. 1993 Jun;57(2):320-46
references.pmid: 8336670
references.citation: Proteomics. 2005 Oct;5(15):3847-50
references.pmid: 16130174
references.citation: Biotechnol Biofuels. 2011 Aug 04;4(1):23
references.pmid: 21816041
references.citation: Mass Spectrom Rev. 2006 May-Jun;25(3):450-82
references.pmid: 16429408
references.citation: J Proteome Res. 2010 Jun 4;9(6):3016-24
references.pmid: 20408570
references.citation: PLoS One. 2011;6(10):e25724
references.pmid: 22022440
references.citation: Biotechniques. 2004 Oct;37(4):621-4, 626-33, 636 passim
references.pmid: 15517975
references.citation: PLoS One. 2012;7(5):e37010
references.pmid: 22649505
references.citation: Prep Biochem. 1994 May;24(2):143-50
references.pmid: 8072956
references.citation: Pac Symp Biocomput. 2006;:315-26
references.pmid: 17094249
references.citation: ACS Chem Biol. 2008 Jan 18;3(1):17-20
references.pmid: 18205287
references.citation: ISME J. 2008 Aug;2(8):853-64
references.pmid: 18449217
references.citation: Stand Genomic Sci. 2011 Oct 15;5(1):69-85
references.pmid: 22180812
references.citation: Appl Environ Microbiol. 2011 Aug 15;77(16):5804-12
references.pmid: 21724886
references.citation: Brief Bioinform. 2010 Jan;11(1):40-79
references.pmid: 19955237
references.citation: Fungal Genet Biol. 2008 May;45(5):638-45
references.pmid: 18308593