Exploring the microbiota dynamics related to vegetable biomasses degradation and study of lignocellulose-degrading bacteria for industrial biotechnological application

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Ventorino, Valeria ^a   Aliberti, Alberto ^a   Faraco, Vincenza ^a   Robertiello, Alessandro ^a   Giacobbe, Simona ^a   Ercolini, Danilo ^a   Amore, Antonella ^a   Fagnano, Massimo ^a   Pepe, Olimpia ^a  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; ENZYME; LIGNIN; LIGNOCELLULOSE; RNA 16S;

BACTERIUM; BIOMASS; CLASSIFICATION; DNA SEQUENCE; ENZYMOLOGY; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; MICROBIOLOGY; MICROFLORA; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRINCIPAL COMPONENT ANALYSIS; VEGETABLE;

BACTERIA; BACTERIAL PROTEINS; BASE SEQUENCE; BIOMASS; ENZYMES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LIGNIN; MICROBIOTA; MOLECULAR SEQUENCE DATA; PHYLOGENY; PRINCIPAL COMPONENT ANALYSIS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; VEGETABLES;

EID: 84945297194     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep08161     Document Type: Article

References (67)

1. Diodato, N., Fagnano, M. & Alberico I. CliFEM - Climate Forcing and Erosion Response Modelling at Long-Term Sele River Research Basin (Southern Italy). Nat. Hazard Earth Syst. Sci. 9, 1693-1702 (2009).
2. Fiorentino, N. et al. Biomass accumulation and heavy metal uptake of giant reed on polluted soil in southern Italy. J. Biotechnol. 150, S1261 (2010).
3. Fiorentino, N. et al. Assisted phytoextraction of heavy metals: compost and Trichoderma effects on giant reed (Arundo donax L) uptake and soil N-cycle microflora. Ital. J. Agron. 8, 244-254 (2013).
4. Pirozzi, D. et al. Lipids production by yeast grown on giant reed biomass. J. Biotechnol. 150, S167-168 (2010).
5. Van Den Burg, B. Extremophiles as a source for novel enzymes. Curr. Opin. Microbiol. 6, 213-218 (2003).
6. Soares, F. L. Jr, Melo, I. S., Dias, A. C. & Andreote, F. D. Cellulolytic bacteria from soils in harsh environments. World J. Microbiol. Biotechnol. 28, 2195-2203 (2012).
7. Maki, M., Leung, K. T. & Qin, W. S. The prospects of cellulase-producing bacteria for the bioconversion of lignocellulosic biomass. Int. J. Biol. Sci. 5, 500-516 (2009).
8. Amore, A. et al. Industrial waste based compost as a source of novel cellulolytic strains and enzymes. FEMS Microbiol. Lett. 339, 93-101 (2013).
9. Sizova, M. V., Izquierdo, J. A., Panikov, N. S. & Lynd, L. R. Cellulose- And xylandegrading thermophilic anaerobic bacteria from biocompost. Appl. Environ. Microbiol. 77, 2282-2291 (2011).
10. Taherzadeh, M. J. & Karimi, K. Enzyme-based hydrolysis processes for ethanol from lignocellulosic materials: A review. Bioresources 2, 707-738 (2007).
11. Saini, J. K. & Tewari, A. L. Simultaneous isolation and screening of cellulolytic bacteria: selection of efficient medium. J. Pure Appl. Microbiol. 3, 1339-1344 (2012).
12. Duan, C. J. & Feng, J. X. Mining metagenomes for novel cellulose genes. Biotechnol. Lett. 32, 1765-1775 (2010).
13. Thompson, C. E. et al. A potential source for cellulolytic enzyme discovery and environmental aspects revealed through metagenomics of Brazilian mangroves. AMB Express 3, 65 (2013).
14. Amore, A. et al. Cloning and recombinant expression of a cellulase from the cellulolytic strain Streptomyces sp. G12 isolated from compost. Microb. Cell Fact. 11, 164 (2012).
15. DeAngelis, K. M. et al. Strategies for enhancing the effectiveness of metagenomicbased enzyme discovery in lignocellulolytic microbial communities. Bioenerg. Res. 3, 146-158 (2010).
16. Kanokratana, P. et al. Insights into the phylogeny and metabolic potential of a primary tropical peat swamp forest microbial community by metagenomic analysis. Microb. Ecol. 61, 518-528 (2011).
17. Van der Heijden, M. G. A., Bardgett, R. D. & van Straalen, N. M. The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol. Lett. 11, 296-310 (2008).
18. DeAngelis, K. M. et al. Characterization of trapped lignin-degrading microbes in tropical forest soil. PLoS ONE 6, e19306 (2011).
19. Wu, Y. R. & He, J. Characterization of anaerobic consortia coupled lignin depolymerization with biomethane generation. Bioresour. Technol. 139C, 5-12 (2013).
20. Matsuyama, T. et al Bacterial community in plant residues in a Japanese paddy field estimated by RFLP and DGGE analyses. Soil Biol. Biochem. 39, 463-472 (2007).
21. Zhang, H. B., Yang, M. X. & Tu, R. Unexpectedly high bacterial diversity in decaying wood of a conifer as revealed by a molecular method. Int. Biodeterior. Biodegrad. 62, 471-474 (2008).
22. Castillo, J. M., Romero, E. & Nogales, R. Dynamics of microbial communities related to biochemical parameters during vermicomposting and maturation of agroindustrial lignocellulose wastes. Bioresour. Technol. 146, 345-354 (2013).
23. Martins, L. F. et al.Metagenomic analysis of a tropical composting operation at the São Paulo Zoo Park reveals diversity of biomass degradation functions and organisms. PLoS ONE 8, e61928 (2013).
24. Lee, Y. J. et al. Purification and characterization of cellulase produced by Bacillus amyoliquefaciens DL-3 utilizing rice hull. Bioresour. Technol. 99, 378-386 (2009).
25. Di Pasqua, R. et al. Influence of different lignocellulose sources on endo-1, 4-ßglucanase gene expression and enzymatic activity of Bacillus amyloliquefaciens B31C. Bioresources 9, 1303-1310 (2014).
26. Kanokratana, P. et al. Phylogenetic analysis and metabolic potential of microbial communities in an industrial bagasse collection site. Microb. Ecol. 66, 322-334 (2013).
27. Stursova, M., Zifcakova, L., Leigh, M. B., Burgess, R. & Baldrian, P. Cellulose utilization in forest litters and soils: identification of bacterial and fungal decomposers. FEMS Microbiol. Ecol. 80, 735-746 (2012).
28. Dalevi, D., Hugenholtz, P. & Blackall, L. L. A multiple-outgroup approach to resolving division-level phylogenetic relationships using16S rDNA data. Int. J. Syst. Evol. Microbiol. 51, 385-391 (2001).
29. Lee, K. C. Y. et al. Phylogenetic Delineation of the Novel Phylum Armatimonadetes (Former Candidate Division OP10) and Definition of Two Novel Candidate Divisions. Appl. Environ. Microbiol. 79, 2484-2487 (2013).
30. Dunfield, P. F. et al. Electing a candidate: A speculative history of the bacterial phylum OP10. Environ. Microbiol. 14, 3069-3080 (2012).
31. Wang, H. et al. Development of microbial populations in the anaerobic hydrolysis of grass silage for methane production. FEMS Microbiol. Ecol. 72, 496-506 (2010).
32. Ventorino, V., Amore, A., Faraco, V., Blaiotta, G. & Pepe, O. Selection of cellulolytic bacteria for processing of cellulosic biomass. J. Biotechnol. 150, S181 (2010).
33. Van Dyk, J. S. & Pletschke, B. I. A review of lignocellulose bioconversion using enzymatic hydrolysis and synergistic cooperation between enzymes - Factors affecting enzymes, conversion and synergy. Biotechnol. Adv. 30, 1458-1480 (2012).
34. Ulrich, K., Ulrich, A. & Ewald, D. Diversity of endophytic bacterial communities in poplar grown under field conditions. FEMS Microbiol. Ecol. 63, 169-180 (2008).
35. Okeke, B. C. & Lu, J. Characterization of a defined cellulolytic and xylanolytic bacterial consortium for bioprocessing of cellulose and hemicelluloses. Appl. Biochem. Biotechnol. 163, 869-881 (2011).
36. Akasaka, H., Izawa, T., Ueki, K. & Ueki, A. Phylogeny of numerically abudant culturable anaerobic bacteria associated with degradation of rice plant residue in Japanese paddy field soil. FEMS Microbiol. Ecol. 43, 149-161 (2003).
37. Lo, Y. C., Saratale, G. D., Chen, W. M., Bai, M. D. & Chang, J. S. Isolation of cellulose-hydrolytic bacteria and applications of the cellulolytic enzymes for cellulosic biohydrogen production. EnzymeMicrob. Technol. 44, 417-425 (2009).
38. Song, J. M. & Wei, D. Z. Production and characterization of cellulases and xylanases of Cellulosimicrobium cellulans grown in pretreated and extracted bagasse and minimal nutrient medium M9. Biomass Bioenerg. 34, 1930-1934 (2010).
39. Zhao, K. et al. Simultaneous saccharification and high titer lactic acid fermentation of corn stover using a newly isolated lactic acid bacterium Pediococcus acidilactici DQ2. Bioresour. Technol. 135, 481-489 (2013).
40. Amore, A., Pepe, O., Ventorino, V., Aliberti, A. & Faraco, V. Cellulolytic Bacillus strains from natural habitats -Areview. Chimica Oggi/Chemistry Today 31, 49-52 (2013).
41. Kim, Y. K., Lee, S. C., Cho, Y. Y., Oh, H. J. & Ko, Y. H. Isolation of cellulolytic Bacillus subtilis strains from agricultural environments. ISRN Microbiol doi: 10.5402/2012/650563 (2012).
42. Jones, S. M., Van Dyk, J. S. & Pletschke, B. I. Bacillus subtilis SJ01 produces hemicellulose degrading multi-enzyme complexes. Bioresources 7, 1294-1309 (2012).
43. Palumbo, J. D., Yuen, G. Y., Jochum, C. C., Tatum, K. & Kobayashi, D. Y. Mutagenesis of ß-1, 3-glucanase genes in Lysobacter enzymogenes strain C3 results in reduced biological control activity toward bipolaris leaf spot of tall fescue and Pythium damping-off of sugar beet. Phytopathology 95, 701-707 (2005).
44. Anand, A. A. et al. Isolation and characterization of bacteria from the gut of Bombyx mori that degrade cellulose, xylan, pectin and starch and their impact on digestion. J. Insect Sci. 10, 107 (2010).
45. Lim, Y. W., Moon, E. Y. & Chun, J. Reclassification of Flavobacterium resinovorum Delaporte and Daste 1956 as Novosphingobium resinovorum comb. nov., with Novosphingobium subarcticum (Nohynek et al. 1996) Takeuchi et al. 2001 as a later heterotypic synonym. Int. J. Syst. Evol. Microbiol. 57, 1906-1908 (2007).
46. Gupta, P., Samant, K. & Sahu, A. Isolation of cellulose-degrading bacteria and determination of their cellulolytic potential. Int. J. Microbiol. doi: 10.1155/2012/578925 (2012).
47. Ekperigin, M. M. Preliminary studies of cellulase production by Acinetobacter anitratus and Branhamella sp. Afr. J. Biotechnol. 6, 28-33 (2007).
48. Ventorino, V., Parillo, R., Testa, A., Aliberti, A. & Pepe, O. Chestnut biomass biodegradation for sustainable agriculture. Bioresources 8, 4647-4658 (2013).
49. Andreotti, R. et al.Assessment of bacterial diversity in the cattle tick Rhipicephalus (Boophilus) microplus through tag-encoded pyrosequencing. BMC Microbiol. 11, 6 (2011).
50. Ercolini, D., De Filippis, F., La Storia, A. & Iacono, M. "Remake" by highthroughput sequencing of the microbiota involved in the production of water buffalo mozzarella cheese. Appl. Environ. Microbiol. 78, 8142-8145 (2012).
51. Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335-336 (2010).
52. Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461 (2010).
53. Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naïve Bayesan classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261-5267 (2007).
54. McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archea. ISME J. 6, 610-618 (2012).
55. Chao, A. & Bunge, J. Estimating the number of species in a stochastic abundance model. Biometrics 58, 531-539 (2002).
56. Shannon, C. E. & Weaver, W. The mathematical theory of communication. Urbana: University of Illinois Press. 125 p. (1949).
57. Saeed, A. I. et al. TM4: A free, opensource system for microarray data management and analysis. Biotechniques 34, 374-378 (2003).
58. Lozupone, C., Hamady, M. & Knight, R. UniFrac e an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7, 371 (2006).
59. Ko, K. C., Han, Y., Shin, B. S., Choi, J. H. & Song, J. J. A rapid and simple method for preparing an insoluble substrate for screening of microbial xylanase. Appl. Biochem. Biotechnol. 167, 677-84 (2012).
60. Pepe, O., Ventorino, V. & Blaiotta, G. Dynamic of functional microbial groups during mesophilic composting of agro-industrial wastes and free-living (N2)- fixing bacteria application. Waste Manage. 33, 1616-1625 (2013).
61. Okino, L. K., Machado, K. G. M., Fabric, C. & Bonomi, V. L. R. Ligninolytic activity of tropical rainforest basidiomycetes. World J. Microbiol. Biotechnol. 16, 889-893 (2000).
62. Toutella, G. R., Rubilar, O., Gianfreda, L., Valenzuela, E. & Diez, M. C. Enzymatic characterization of Chilean native wood-rotting fungi for potential use in the bioremediation of polluted environment with chlorophenols. World J. Microbiol. Biotechnol. 24, 2805-2818 (2008).
63. Pointing, S. B. Qualitative methods for the determination of lignocellulolytic enzyme production by tropical fungi. Fungal Divers. 2, 17-33 (1999).
64. Alfonzo, A. et al. Antifungal peptides produced by Bacillus amyloliquefaciens AG1 active against grapevine fungal pathogens. Ann.Microbiol. 62, 1593-1599 (2012).
65. Pepe, O. et al. Characterization in the archaeological excavation site of heterotrophic bacteria and fungi of deteriorated wall painting of Herculaneum in Italy. J. Environ. Biol. 32, 241-250 (2011).
66. Thompson, J. D., Higgins, D. G. & Gibson, T. J. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weightmatrix choice. Nucleic Acids Res. 22, 4673-4680 (1994).
67. Tamura, K., Dudley, J., Nei, M. & Kumar, S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596-1599 (2007).