Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities

Biotechnology for Biofuels

Volumn 8, Issue 1, 2015, Pages

  Mhuantong, Wuttichai ^a   Charoensawan, Varodom ^b,c   Kanokratana, Pattanop ^a   Tangphatsornruang, Sithichoke ^a   Champreda, Verawat ^a  

^a NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY   (Thailand)

^b Mahidol University   (Thailand)

^c MAHIDOL UNIVERSITY   (Thailand)

Author keywords

Biofuels; Biorefinery; Comparative genomics; Lignocellulose degradation; Metagenomics

Indexed keywords

AGRICULTURAL WASTES; BIOFUELS; BIOMASS; CELLULOSE; CONSERVATION; ENZYMES; GENES; HYDROLASES; LIGNIN; MICROORGANISMS; PLANTS (BOTANY); REFINING; SUGARS;

BIOREFINERIES; COMPARATIVE GENOMICS; FUNCTIONAL CHARACTERIZATION; LIGNOCELLULOLYTIC ENZYMES; LIGNOCELLULOSE DEGRADATION; METAGENOMICS; MICROBIAL COMMUNITIES; TAXONOMIC COMPOSITION;

BAGASSE;

BIODEGRADATION; BIOFUEL; BIOTECHNOLOGY; CELLULOSE; COMPARATIVE STUDY; ENZYME ACTIVITY; GENOME; MICROBIAL COMMUNITY; SUGAR CANE;

PROTEOBACTERIA;

EID: 84924228652     PISSN: 17546834     EISSN: None     Source Type: Journal    
DOI: 10.1186/s13068-015-0200-8     Document Type: Article

References (62)

1. Van Dyk JS, Pletschke BI. A review of lignocellulose bioconversion using enzymatic hydrolysis and synergistic cooperation between enzymes - factors affecting enzymes, conversion and synergy. Biotechnol Adv. 2012;30(6):1458-80.
2. Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev. 2002;66(3):506-77.
3. Rubin EM. Genomics of cellulosic biofuels. Nature. 2008;454(7206):841-5.
4. Lee J. Biological conversion of lignocellulosic biomass to ethanol. J Biotechnol. 1997;56(1):1-24.
5. Kanokratana P, Mhuantong W, Laothanachareon T, Tangphatsornruang S, Eurwilaichitr L, Pootanakit K, et al. Phylogenetic analysis and metabolic potential of microbial communities in an industrial bagasse collection site. Microb Ecol. 2013;66(2):322-34.
6. Weimann A, Trukhina Y, Pope PB, Konietzny SG, McHardy AC. De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-) genomes. Biotechnol Biofuels. 2013;6(1):24.
7. Li LL, McCorkle SR, Monchy S, Taghavi S, van der Lelie D. Bioprospecting metagenomes: glycosyl hydrolases for converting biomass. Biotechnol Biofuels. 2009;2:10.
8. Rattanachomsri U, Kanokratana P, Eurwilaichitr L, Igarashi Y, Champreda V. Culture-independent phylogenetic analysis of the microbial community in industrial sugarcane bagasse feedstock piles. Biosci Biotechnol Biochem. 2011;75(2):232-9.
9. Alvarez TM, Goldbeck R, dos Santos CR, Paixao DA, Goncalves TA, Franco Cairo JP, et al. Development and biotechnological application of a novel endoxylanase family GH10 identified from sugarcane soil metagenome. PLoS One. 2013;8(7):e70014.
10. Sangwan N, Lata P, Dwivedi V, Singh A, Niharika N, Kaur J, et al. Comparative metagenomic analysis of soil microbial communities across three hexachlorocyclohexane contamination levels. PLoS One. 2012;7(9):e46219.
11. Shi W, Xie S, Chen X, Sun S, Zhou X, Liu L, et al. Comparative genomic analysis of the microbiome [corrected] of herbivorous insects reveals eco-environmental adaptations: biotechnology applications. PLoS Genet. 2013;9(1):e1003131.
12. Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, et al. Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci U S A. 2009;106(5):1374-9.
13. Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL, et al. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci U S A. 2012;109(52):21390-5.
14. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, et al. Comparative metagenomics of microbial communities. Science. 2005;308(5721):554-7.
15. Kanokratana P, Uengwetwanit T, Rattanachomsri U, Bunterngsook B, Nimchua T, Tangphatsornruang S, et al. Insights into the phylogeny and metabolic potential of a primary tropical peat swamp forest microbial community by metagenomic analysis. Microb Ecol. 2011;61(3):518-28.
16. Brulc JM, Antonopoulos DA, Miller ME, Wilson MK, Yannarell AC, Dinsdale EA, et al. Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci U S A. 2009;106(6):1948-53.
17. Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, et al. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science. 2011;331(6016):463-7.
18. Pope PB, Denman SE, Jones M, Tringe SG, Barry K, Malfatti SA, et al. Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proc Natl Acad Sci U S A. 2010;107(33):14793-8.
19. Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, et al. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature. 2007;450(7169):560-5.
20. Martins LF, Antunes LP, Pascon RC, de Oliveira JC, Digiampietri LA, Barbosa D, et al. Metagenomic analysis of a tropical composting operation at the Sao Paulo zoo park reveals diversity of biomass degradation functions and organisms. PLoS One. 2013;8(4):e61928.
21. Lamendella R, Domingo JW, Ghosh S, Martinson J, Oerther DB. Comparative fecal metagenomics unveils unique functional capacity of the swine gut. BMC Microbiol. 2011;11:103.
22. Wongwilaiwalin S, Laothanachareon T, Mhuantong W, Tangphatsornruang S, Eurwilaichitr L, Igarashi Y, et al. Comparative metagenomic analysis of microcosm structures and lignocellulolytic enzyme systems of symbiotic biomass-degrading consortia. Appl Microbiol Biotechnol. 2013;97(20):8941-54.
23. Pruitt KD, Tatusova T, Brown GR, Maglott DR. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res. 2012;40(Database issue):D130-135.
24. Morrison M, Pope PB, Denman SE, McSweeney CS. Plant biomass degradation by gut microbiomes: more of the same or something new? Curr Opin Biotechnol. 2009;20(3):358-63.
25. Larsbrink J, Rogers TE, Hemsworth GR, McKee LS, Tauzin AS, Spadiut O, et al. A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes. Nature. 2014;506(7489):498-502.
26. Fernandez AB, Vera-Gargallo B, Sanchez-Porro C, Ghai R, Papke RT, Rodriguez-Valera F, et al. Comparison of prokaryotic community structure from Mediterranean and Atlantic saltern concentrator ponds by a metagenomic approach. Front Microbiol. 2014;5:196.
27. Patel DD, Patel AK, Parmar NR, Shah TM, Patel JB, Pandya PR, et al. Microbial and Carbohydrate Active Enzyme profile of buffalo rumen metagenome and their alteration in response to variation in the diet. Gene. 2014;545(1):88-94.
28. Park SK, Jang HM, Ha JH, Park JM. Sequential sludge digestion after diverse pre-treatment conditions: sludge removal, methane production and microbial community changes. Bioresource Technol. 2014;162:331-40.
29. Hollister EB, Forrest AK, Wilkinson HH, Ebbole DJ, Tringe SG, Malfatti SA, et al. Mesophilic and thermophilic conditions select for unique but highly parallel microbial communities to perform carboxylate platform biomass conversion. PLoS One. 2012;7(6):e39689.
30. Levasseur A, Drula E, Lombard V, Coutinho PM, Henrissat B. Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. Biotechnol Biofuels. 2013;6(1):41.
31. Kodama Y, Shumway M, Leinonen R. The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res. 2012;40(Database issue):D54-56.
32. Allgaier M, Reddy A, Park JI, Ivanova N, D'Haeseleer P, Lowry S, et al. Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS One. 2010;5(1):e8812.
33. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, et al. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312(5778):1355-9.
34. Garcia Martin H, Ivanova N, Kunin V, Warnecke F, Barry KW, McHardy AC, et al. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nature Biotechnol. 2006;24(10):1263-9.
35. Dougherty MJ, D'Haeseleer P, Hazen TC, Simmons BA, Adams PD, Hadi MZ. Glycoside hydrolases from a targeted compost metagenome, activityscreening and functional characterization. BMC Biotechnol. 2012;12:38.
36. Gladden JM, Park JI, Bergmann J, Reyes-Ortiz V, D'Haeseleer P, Quirino BF, et al. Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community. Biotechnol Biofuels. 2014;7(1):15.
37. Dassa B, Borovok I, Ruimy-Israeli V, Lamed R, Flint HJ, Duncan SH, et al. Rumen cellulosomics: divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains. PLoS One. 2014;9(7):e99221.
38. Martens EC, Kelly AG, Tauzin AS, Brumer H: The devil lies in the details: how variations in polysaccharide fine-structure impact the physiology and evolution of gut microbes. J Molecular Biol. 2014.
39. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444(7122):1027-31.
40. Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell. 2006;124(4):837-48.
41. Thomas F, Hehemann JH, Rebuffet E, Czjzek M, Michel G. Environmental and gut Bacteroidetes: the food connection. Frontiers Microbiol. 2011;2:93.
42. Brune A, Emerson D, Breznak JA. The termite gut microflora as an oxygen sink: microelectrode determination of oxygen and pH gradients in guts of lower and higher termites. Appl Environmental Microbiol. 1995;61(7):2681-7.
43. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003;4:41.
44. Sekelja M, Rud I, Knutsen SH, Denstadli V, Westereng B, Naes T, et al. Abrupt temporal fluctuations in the chicken fecal microbiota are explained by its gastrointestinal origin. Appl Environmental Microbiol. 2012;78(8):2941-8.
45. Charoensawan V, Wilson D, Teichmann SA. Genomic repertoires of DNA-binding transcription factors across the tree of life. Nucleic Acids Res. 2010;38(21):7364-77.
46. Charoensawan V, Wilson D, Teichmann SA. Lineage-specific expansion of DNA-binding transcription factor families. Trends Genetics: TIG. 2010;26(9):388-93.
47. Maslov S, Krishna S, Pang TY, Sneppen K. Toolbox model of evolution of prokaryotic metabolic networks and their regulation. Proc Natl Acad Sci U S A. 2009;106(24):9743-8.
48. Nakaya A, Katayama T, Itoh M, Hiranuka K, Kawashima S, Moriya Y, et al. KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. Nucleic Acids Res. 2013;41(Database issue):D353-357.
49. Hu J, Arantes V, Pribowo A, Saddler JN. The synergistic action of accessory enzymes enhances the hydrolytic potential of a "cellulase mixture" but is highly substrate specific. Biotechnol Biofuels. 2013;6(1):112.
50. Langston JA, Shaghasi T, Abbate E, Xu F, Vlasenko E, Sweeney MD. Oxidoreductive cellulose depolymerization by the enzymes cellobiose dehydrogenase and glycoside hydrolase 61. Appl Environmental Microbiol. 2011;77(19):7007-15.
51. Berka RM, Grigoriev IV, Otillar R, Salamov A, Grimwood J, Reid I, et al. Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris. Nature Biotechnol. 2011;29(10):922-7.
52. Eastwood DC, Floudas D, Binder M, Majcherczyk A, Schneider P, Aerts A, et al. The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi. Science. 2011;333(6043):762-5.
53. Harris PV, Welner D, McFarland KC, Re E, Navarro Poulsen JC, Brown K, et al. Stimulation of lignocellulosic biomass hydrolysis by proteins of glycoside hydrolase family 61: structure and function of a large, enigmatic family. Biochemistry. 2010;49(15):3305-16.
54. Kiatkittipong W, Wongsuchoto P, Pavasant P. Life cycle assessment of bagasse waste management options. Waste Manag. 2009;29(5):1628-33.
55. Kanokratana P, Eurwilaichitr L, Pootanakit K, Champreda V: Identification of glycosyl hydrolases from a metagenomic library of microflora in sugarcane bagasse collection site and their cooperative action on cellulose degradation. J Bioscience Bioengineering. 2014.
56. Zhou J, Bruns MA, Tiedje JM. DNA recovery from soils of diverse composition. Appl Environ Microbiol. 1996;62(2):316-22.
57. Kanokratana P, Chanapan S, Pootanakit K, Eurwilaichitr L. Diversity and abundance of Bacteria and Archaea in the Bor Khlueng Hot Spring in Thailand. J Basic Microbiol. 2004;44(6):430-44.
58. Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28(23):3150-2.
59. Zhu W, Lomsadze A, Borodovsky M. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res. 2010;38(12):e132.
60. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, communitysupported software for describing and comparing microbial communities. Appl Environmental Microbiol. 2009;75(23):7537-41.
61. Conesa A, Gotz S. Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics. 2008;2008:619832.
62. Kalyuzhnaya MG, Lidstrom ME, Chistoserdova L. Real-time detection of actively metabolizing microbes by redox sensing as applied to methylotroph populations in Lake Washington. ISME J. 2008;2(7):696-706.