Shift in microbial population in response to crystalline cellulose degradation during enrichment with a semi-desert soil

International Biodeterioration and Biodegradation

Volumn 88, Issue , 2014, Pages 134-141

  Kumar, Mohit ^a   Khanna, Sunil ^a  

^a NIIT University   (India)

Author keywords

16S rRNA; Crystalline cellulose; Glycosyl hydrolase; Semi desert soil community

Indexed keywords

16S RRNA; 16S RRNA GENE SEQUENCE; BACTERIAL POPULATION; CRYSTALLINE CELLULOSE; FUNCTIONAL DIVERSITY; GLYCOSYL HYDROLASES; MICROBIAL POPULATIONS; SOIL COMMUNITY;

BACTERIOLOGY; CELLULOSE; GENES; HYDROLASES; LANDFORMS; RNA; SOILS;

CRYSTALLINE MATERIALS;

CELLULOSE; DEGRADATION; ENRICHMENT; ENZYME; GENE; RELATIVE ABUNDANCE; SOIL;

EID: 84892415874     PISSN: 09648305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ibiod.2013.10.025     Document Type: Article

References (39)

1. Aa K., Flengsrud R., Lindahl V., Tronsmo A. Characterisation of production and enzyme properties of an endo-β-1,4-glucanase from Bacillus subtilis CK-2 isolated from compost soil. Ant. Van Leeuwenhoek 1994, 66:319-326.
2. Amann R.J., Binder B.L., Chisholm S.W., Devereux R., Stahl D.A. Combination of 16S rRNA targeted oligonucleotide probes with flow-cytometry for analysing mixed microbial populations. Appl. Environ. Microbiol. 1990, 56:1919-1925.
3. Bayer E.A., Belaich J.-P., Shoham Y., Lamed R. The cellulosomes: multienzyme machines for degradation of plant cell Wall polysaccharides. Annu. Rev. Microbiol. 2004, 58:521-554.
4. Begon M., Harper J.L., Townsend C.R. Ecology: Individuals, Populations and Communities. Bioinformatics 1990, vol. 5:150-163. Blackwell Scientific Publications, Oxford.
5. Braker G., Zhou J., Wu L., Devol A.H., Tiedje J.M. Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in Pacific Northwest marine sediment communities. Appl. Environ. Microbiol. 2000, 66:2096-2104.
6. Chao A., Lee S.M. Estimating the number of classes via sample coverage. JAm. Stat. Assoc. 1992, 87:210-217.
7. Colwell R.K., Mao C.X., Chang J. Interpolating, extrapolating and comparing incidence based species accumulation curves. Ecology 2004, 85:2717-2727.
8. Cottrell M.T., Wood D.N., Yu L., Kirchman D.L. Selected chitinase genes in cultured and uncultured marine bacteria in the α- and γ- subclasses of the Proteobacteria. Appl. Environ. Microbiol. 2000, 66:1195-1201.
9. De Boer W., Leveau J.H.L., Kowalchuk G.A., Paulien J.A., Klein G., Abeln Edwin C.A., Marian J.F., Klaas S., Jaap D.J., van V Johannes A. Collimonas fungivorans gen. nov., sp. nov. a chitinolytic soil bacterium with the ability to grown on living fungal hyphae. Int. J. Syst. Evol. Microbiol. 2004, 54:857-864.
10. Doyle J., Pavel R., Barness G., Steinberger Y. Cellulase dynamics in desert soil. Soil. Biol. Biochem. 2006, 38:371-376.
11. Edwards J.L., Smith D.L., Connolly J., Mcdonald J.E., Cox M.J., Joint I., Edwards C., Mccarthy A.J. Identification of carbohydrate metabolism genes in the metagenome of a marine biofilm community shown to be dominated by gammaproteobacteria and bacteroidetes. Genes 2010, 1:371-384.
12. Huang D.L., Zeng G.M., Feng C.L., Hu S., Lai C., Mei-Hua Z., Feng-Feng S., Lin T., Hong-Liang L. Changes of microbial population structure related to lignin degradation during lignocellulosic waste composting. Bioresour. Technol. 2010, 101:4062-4067.
13. Ito S., Kobayashi T., Ara K., Ozaki K., Kawai S., Hatada Y. Alkaline detergent enzymes from alkaliphiles: enzymatic properties, genetics, and structures. Extremophiles 1998, 2:185-190.
14. Izquierdo J.A., Sizova M.V., Lynd L.R. Diversity of bacteria and glycosyl hydrolase family 48 genes in cellulolytic consortia enriched from thermophilic biocompost. Appl. Environ. Microbiol. 2010, 76:3545-3553.
15. Jacobsen J., Lydolph M., Lange L. Culture independent PCR: an alternative enzyme discovery strategy. J.Microbiol. Methods 2005, 60:63-71.
16. Koga K., Suehiro Y., Shun-Taro M., Katsutada T. Evaluation of growth activity of microbes in tea field soil using microbial calorimetry. J.Biosci. Bioeng. 2003, 95:429-434.
17. Kumar M., Khanna S. Diversity of 16S rRNA and dioxygenase genes detected in coal-tar-contaminated site undergoing active bioremediation. J.Appl. Microbiol. 2010, 108:1252-1262.
18. Kumar M., Joshi A., Kashyap R., Khanna S. Production of xylanase by Promicromonospora sp MARS with rice straw under non sterile conditions. Process Biochem. 2011, 46:1614-1618.
19. Kumar S., Nei M., Dudley J., Tamura K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings Bioinforma. 2008, 9:299-306.
20. Li L.L., McCorkle S.M., Monchy S., Taghavi S., van der Lelie D. Bioprospecting metagenomes: glycosyl hydrolases for converting biomass. Biotechnol. Biofuels 2009, 2:10.
21. LeCleir G.R., Buchan A., Hollibaugh J.T. Chitinase gene sequences retrieved from diverse aquatic habitats reveal environment-specific distributions. Appl. Environ. Microbiol. 2004, 70:6977-6983.
22. Lednicka D., Mergaert J., Cnockaert M.C., Swings J. Isolation and identification of cellulolytic bacteria involved in the degradation of natural cellulosic fibres. Syst. Appl. Microbiol. 2000, 23:292-299.
23. Lee Y.J., Kim B.K., Lee B.H., Jo K.I., Lee N.K., Chung C.H., Lee Y.C., Lee J.W. Purifcation characterization of cellulase produced by Bacillus amyoliquefaciens DL-3 utilizing rice hull. Bioresour. Technol. 2008, 99:378-386.
24. Mawadza C., Hatti-Kaul R., Zvauya R., Mattiasson B. Purification and characterization of cellulases produced by two Bacillus strains. J.Biotechnol. 2000, 83:177-187.
25. Monteiro R.A., Schmidt M.A., Baura V.A., Balsanelli E., Wassem R., Yates M.G., Randi M.A.F., Pedrosa F.O., de Souza E.M.I. Early colonization pattern of maize (Zea mays L. Poales, Poaceae) roots by Herbaspirillum seropedicae (Burkholderiales, Oxalobacteraceae). Genet. Mol. Biol. 2008, 31:932-937.
26. Ogawa A., Suzumatsu A., Takizawa S., Kubota H., Sawada K., Hakamada Y., Kawai S., Kobayashi T., Ito S. Endoglucanases from Paenibacillus spp. form a new clan in glycoside hydrolase family 5. J.Biotechnol. 2007, 129:406-414.
27. Ozaki K., Ito S. Purification and properties of an acid endo-β-1,4-glucanase from Bacillus sp KSM-330. J.General Microbiol. 1991, 137:41-48.
28. Pielou E.C. Mathematical Ecology 1977, Wiley, New York.
29. Rastogi G., Muppidi G.L., Gurram R.N., Adhikari A., Bischoff K.M., Hughes S.R., Apel W.A., Bang S.S., Dixon D.J., Sani R.K. Isolation charactization of cellulose-degrading bacteria from the deep subsurface of the Homestake gold mine, Lead, South Dakota, USA. J.Ind. Microbiol. Biotechnol. 2009, 36:585-598.
30. Ringelberg D.B., Talley J.W., Perkins E.J., Tucker S.G., Luthy R.G., Bouwer E.J., Fredrickson H.L. Succession of phenotypic, genotypic, and metabolic community characteristics during invitro bioslurry treatment of polycyclic aromatic hydrocarbon-contaminated sediments. Appl. Environ. Microbiol. 2001, 67:1542-1550.
31. Rose T., Schultz E., Henikoff J., Pietrokovski S., McCallum C., Henikoff S. Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences. Nucleic Acids Res. 1998, 26:1628-1635.
32. Sambrook J., Fritsch E.F., Maniatis T. Molecular Cloning - a Laboratory Manual 1987, Cold Spring Harbor, New York.
33. Taylor E.C. Role of aerobic microbial populations in cellulose digestion by desert millipedes. Appl. Environ. Microbiol. 1982, 44:281-291.
34. van der Lelie D., Taghavi S., McCorkle S.M., Li L.-L., Malfatti S.A., Monteleone D., Donohoe B.S., Ding Shi-You., Adney W.S., Himmel M.E., Tringe S.G. The metagenome of an anaerobic microbial community decomposing poplar wood chips. PLoS ONE 2012, 7:e36740. 10.1371/journal.pone.0036740.
35. Velichkov A.D. Asimple procedure for dissolving fungal cell wall preparations for the analysis of neutral sugars. World J. Microbiol. Biotechnol. 1992, 8:527-528.
36. Wang C.M., Shyu C.L., Ho S.P. Characterization of a novel thermophilic cellulose degrading bacterium - Paenibacillus spp strain B39. Lett. Appl. Microbiol. 2008, 47:46-53.
37. Xiang Q., Lee Y.Y., Pettersson P.O., Torget R.W. Heterogeneous aspectsof acid hydrolysis of alpha-cellulose. Appl. Biochem. Biotechnol. 2003, 108:505-514.
38. Yu H., Zeng G., Huang H., Xi X., Wang R., Huang D., Huang G., Li J. Microbial community succession and lignocellulose degradation during agricultural waste composting. Biodegradation 2007, 18:793-802.
39. Zhu Y., Li H., Zhou H., Chen G., Liu W. Cellulose and cellodextrin utilization by the cellulolytic bacterium Cytophaga hutchisonii. Bioresour. Technol. 2010, 101:6432-6437.