Metaproteomic analysis of ratoon sugarcane rhizospheric soil

BMC Microbiology

Volumn 13, Issue 1, 2013, Pages

  Lin, Wenxiong ^a   Wu, Linkun ^a   Lin, Sheng ^a   Zhang, Aijia ^a   Zhou, Mingming ^a   Lin, Rui ^b   Wang, Haibin ^a   Chen, Jun ^a   Zhang, Zhixing ^a   Lin, Ruiyu ^a  

^a FUJIAN AGRICULTURE AND FORESTRY UNIVERSITY   (China)

^b XIAMEN UNIVERSITY   (China)

Author keywords

2D electrophoresis; CLPP; Soil enzyme; Soil metaproteomics; Soil protein extraction; Sugarcane

Indexed keywords

6 PHOSPHOFRUCTOKINASE; ACYL COENZYME A DEHYDROGENASE; AMINO ACID; AUXIN; BETA FRUCTOFURANOSIDASE; BETAINE ALDEHYDE DEHYDROGENASE; CARBOHYDRATE; CARBON; CATALASE; GAMMA TUBULIN; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE CYTOSOLIC 3; NITRATE REDUCTASE; NITRATE REDUCTASE ALPHA SUBUNIT; NITROGEN; NUCLEOTIDE; OXIDOREDUCTASE; PEROXIDASE; PHOSPHATASE; PHOSPHOGLYCERATE KINASE; PHOSPHORUS; PROTEASOME; PROTEASOME BETA TYPE 1; PROTEIN; PROTEOME; SUCCINATE DEHYDROGENASE; SUCCINATE DEHYDROGENASE (UBIQUINONE); SUCROSE; UNCLASSIFIED DRUG; UREASE; URIDINE DIPHOSPHATE GLUCOSE DEHYDROGENASE;

AMINO ACID METABOLISM; ARTICLE; ENERGY; ENZYME ACTIVITY; MEMBRANE TRANSPORT; MICROBIAL COLONIZATION; NONHUMAN; PLANT STEM; PROTEIN EXPRESSION; PROTEOMICS; RHIZOSPHERIC MICROORGANISM; SIGNAL TRANSDUCTION; SOIL; SOIL ANALYSIS; SOIL MICROFLORA; SUGARCANE; UPREGULATION;

ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; PROTEOME; PROTEOMICS; RHIZOSPHERE; SACCHARUM; SOIL; SOIL MICROBIOLOGY; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 84879044335     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-13-135     Document Type: Article

References (68)

1. A model of the stubble replacement decision for Florida sugarcane growers. Crane DR Jr, Spreen TH, South J Agr Econ 1980 12 55 63
2. Improving rhizospheric environment and sugarcane ratoon yield through bioagents amended farm yard manure in udic ustochrept soil. Shukla SK, Yadav RL, Suman A, Singh PN, Soil Till Res 2008 99 158 168 10.1016/j.still.2008.02.007
3. New dimensions in agroecology. Lin WX, Chen T, Zhou MM, Chinese Journal of Eco-Agriculture 2012 20 253 264 10.3724/SP.J.1011.2012.00253
4. The yield plateau in the Australian sugar industry: 1970-1990. Garside AL, Smith MA, Chapman LS, Hurney AP, Magarey RC, Intensive sugarcane production, meeting the challenges beyond 2000 Wallingford: CAB International, Keating BA, Wilson JR, 1997 103 124
5. Residual effect of germination temperature in sugarcane. Gascho GJ, Ruelke OC, West SH, Crop Sci 1973 13 274 276 10.2135/cropsci1973. 0011183X001300020037x
6. Microbiological aspects of sugarcane yield decline. Magarey RC, Aust J Agr Res 1996 47 307 322 10.1071/AR9960307
7. Management practices to improve soil health and reduce the effects of detrimental soil biota associated with yield decline of sugarcane in Queensland. Pankhurst CE, Magarey RC, Stirling GR, Blair BL, Bell MJ, Garside AL, Soil Till Res 2003 72 125 137 10.1016/S0167-1987(03)00083-7
8. Effect of rotation breaks and organic matter amendments on the capacity of soils to develop biological suppression towards soil organisms associated with yield decline of sugarcane. Pankhurst CE, Blair BL, Magarey RC, Stirling GR, Bell MJ, Garside AL, Appl Soil Ecol 2005 28 271 282 10.1016/j.apsoil.2004. 07.010
9. Changes in nematode populations on sugarcane following fallow, fumigation and crop rotation, and implications for the role of nematodes in yield decline. Stirling GR, Blair BL, Pattemore JA, Garside AL, Bell MJ, Australas Plant Path 2001 30 323 335 10.1071/AP01044
10. Plant-microbe interactions in the rhizosphere and nutrient cycling. Marschner P, Nutrient cycling in terrestrial ecosystems. Volume 10 Berlin: Springer, Marschner P, Rengel Z, 2007 159 182
11. Exploring the plant-associated bacterial communities in Medicago sativa L. Pini F, Frascella A, Santopolo L, Bazzicalupo M, Biondi EG, Scotti C, Mengoni A, BMC Microbiol 2012 12 78 10.1186/1471-2180-12-78 22607312
12. Rhizosphere biology- an overview. Mukerji KG, Manoharachary C, Microbial activity in the rhizosphere. Volume 7 Berlin: Springer, Mukerji KG, Manoharachary C, Singh J, 2006 1 39
13. T-RFPred: a nucleotide sequence size prediction tool for microbial community description based on terminal-restriction fragment length polymorphism chromatograms. Fernàndez-Guerra A, Buchan A, Mou X, Casamayor EO, González JM, BMC Microbiol 2010 10 262 10.1186/1471-2180-10-262 20950425
14. Dynamic changes of microbial community diversity in a photohydrogen producing reactor monitored by PCR-DGGE. Ying Y, Lv Z, Min H, Cheng J, J Environ Sci 2008 20 1118 1125 10.1016/S1001-0742(08)62158-0
15. Quantification of mRNA in Salmonella sp. seeded soil and chicken manure using magnetic capture hybridization RT-PCR. Jacobsen C, Holben W, J Microbiol Methods 2007 69 315 321 10.1016/j.mimet.2007.02.001 17383760
16. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Griffin TJ, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R, Mol Cell Proteomics 2002 1 323 333 10.1074/mcp.M200001-MCP200 12096114
17. Characterization of metaproteomics in crop rhizospheric soil. Wang HB, Zhang ZX, Li H, He HB, Fang CX, Zhang AJ, Li QS, Chen RS, Guo XK, Lin HF, Wu LK, Lin S, Chen T, Lin RY, Peng XX, Lin WX, J Proteome Res 2011 10 932 940 10.1021/pr100981r 21142081
18. Metaproteomics: a new approach for studying functional microbial ecology. Maron PA, Ranjard L, Mougel C, Lemanceau P, Microb Ecol 2007 53 486 493 10.1007/s00248-006-9196-8 17431707
19. Microbial protein in soil: Influence of extraction method and C amendment on extraction and recovery. Taylor E, Williams M, Microb Ecol 2010 59 390 399 10.1007/s00248-009-9593-x 19844650
20. Soil bacterial functional diversity as influenced by organic amendment application. Gomez E, Ferreras L, Toresani S, Bioresour Technol 2006 97 1484 1489 10.1016/j.biortech.2005.06.021 16168637
21. Proteomic profiling of dog urine after European adder (Vipera berus berus) envenomation by two-dimensional difference gel electrophoresis. Palviainen M, Raekallio M, Vainionpää M, Kosonen S, Vainio O, Toxicon 2012 60 1228 1234 10.1016/j.toxicon.2012.08.010 22975087
22. Soil microbial community composition and diversity in the rhizosphere of a Chinese medicinal plant. Qi JJ, Yao HY, Ma XJ, Zhou LL, Li XN, Commun Soil Sci Plan 2009 40 1462 1482 10.1080/00103620902818104
23. Effect of monoculture soybean on soil microbial community in the Northeast China. Li CG, Li XM, Kong WD, Wu Y, Wang JG, Plant Soil 2010 330 423 433 10.1007/s11104-009-0216-6
24. Effect of amendments with different phenolic acids on soil microbial biomass, activity, and community diversity. Qu XH, Wang JG, Appl Soil Ecol 2008 39 172 179 10.1016/j.apsoil.2007.12.007
25. Effect of cinnamic acid on soil microbial characteristics in the cucumber rhizosphere. Wu FZ, Wang XZ, Xue CY, Eur J Soil Biol 2009 45 356 362 10.1016/j.ejsobi.2009.04.001
26. Hunsigi G, Sugarcane in Agriculture and Industry Bangalore: Prism Books Pvt Ltd 2001
27. Rotation-induced changes in soil biological properties and their effect on yield decline in sugarcane. Pankhurst CE, Magarey RC, Stirling GR, Holt JA, Brown JD, Proc Aust Soc Sugar Cane Technol 1999 21 79 86
28. Microbial interactions and biocontrol in the rhizosphere. Whipps JM, J Exp Bot 2001 52 487 511 10.1093/jexbot/52.suppl-1.487 11326055
29. Enzyme activities and metabolic profiles of soil microorganisms at KILN sites in Quercus spp. temperate forests of central Mexico. Gómez-Luna BE, De la Luz Ruiz-Aguilar GM, Vázquez-Marrufo G, Dendooven L, Olalde-Portugal V, Appl Soil Ecol 2012 52 48 55
30. Development and validation of numerical indexes integrating enzyme activities of soils. Puglisi E, Del Re AAM, Rao MA, Gianfreda L, Soil Biol Biochem 2006 38 1673 1681 10.1016/j.soilbio.2005.11.021
31. Reproducibility in the response of soil bacterial community-level physiological profiles from a land use intensification gradient. Gomez E, Garland J, Conti M, Appl Soil Ecol 2004 26 21 30 10.1016/j.apsoil.2003.10.007
32. Functional diversity of soil bacteria as affected by management practices and phenological stage of Phaseolus vulgaris. Papatheodorou EM, Efthimiadou E, Stamou GP, Eur J Soil Biol 2008 44 429 436 10.1016/j.ejsobi.2008.06.002
33. Analysis of microbial community functional diversity using sole-carbonsource utilization profiles-a critique. Preston-Mafham J, Boddy L, Randerson PF, FEMS Microb Ecol 2002 42 1 14
34. Root Exudates as determinant of rhizospheric microbial biodiversity. Singh G, Mukerji KG, Microbial activity in the rhizosphere. Volume 7 Berlin: Springer, Mukerji KG, Manoharachary C, Singh J, 2006 39 53
35. Plant root carbohydrates affect growth behaviour of endophytic microfungi. Hadacek F, Gunther FF, FEMS Microbiol Ecol 2002 41 161 170 10.1111/j.1574-6941.2002.tb00977.x 19709250
36. Foyer CH, Mullineaux PM, Causes of photooxidative stres and amelioration of defense dystems in Plants Boca Raton: CRC Press 1994
37. Active oxygen in plant pathogenesis. Baker CJ, Orlandi EW, Annu Rev Phytopathol 1995 33 299 321 10.1146/annurev.py.33.090195.001503 18999963
38. The chloroplast small heat shock protein undergoes oxidation-dependent conformational changes and may protect plants from oxidative stress. Härndahl U, Hall RB, Osteryoung KW, Vierling E, Bornman JF, Sundby C, Cell Stress Chaperon 1999 4 129 138 10.1379/1466-1268(1999)004<0129:TCSHSP>2.3. CO;2
39. rbohA, a rice homologue of the mammalian gp91phox respiratory burst oxidase gene. Groom QJ, Torres MA, Fordham-Skelton AP, Hammond-Kosack KE, Robinson NJ, Jones JD, Plant J 1996 10 515 522 10.1046/j.1365-313X.1996. 10030515.x 8811865
40. Pseudomonas syringae hijacks plant stress chaperone machinery for virulence. Jelenska J, van Hal JA, Greenberg JT, PNAS 2010 107 13177 13182 10.1073/pnas.0910943107 20615948
41. Genes expressed in pinus radiata male cones include homologs to anther-specific and pathogenesis response genes. Walden AR, Walter C, Gardner RC, Plant Physiol 1999 121 1103 1116 10.1104/pp.121.4.1103 10594098
42. hsr203J, a tobacco gene whose activation is rapid, highly localized and specific for incompatible plant/pathogen interactions. Pontier D, Godiard L, Marco Y, Roby D, Plant J 1994 5 507 521 10.1046/j.1365-313X.1994.5040507.x 8012404
43. Genome-wide gene responses in a transgenic rice line carrying the maize resistance gene Rxo1 to the rice bacterial streak pathogen, Xanthomonas oryzae pv. Oryzicola. Zhou YL, Xu MR, Zhao MF, Xie XW, Zhu LH, Fu BY, Li ZK, BMC Genomics 2010 11 78 10.1186/1471-2164-11-78 20122142
44. Yield decline of sugarcane. Magarey RC, Current trends in sugarcane pathology Pitampura: International Books and Periodicals Supply Service, Rao GP, Gillaspie AGJr, Upadhyaya PP, Bergamin A, Agnihotri VP, Chen CT, 1994 393 412
45. Nematode pests: their role in yield decline of sugarcane and opportunities for improved management practices. Stirling GR, Blair BL, Whittle PJL, Sugarcane: Research towards efficient and sustainable production Brisbane: CSIRO Division of Tropical Crops and Pastures, Wilson JR, Hogarth DM, Campbell JA, Garside AL, 1996 228 229
46. Cellodextrin and laminaribiose ABC transporters in Clostridium thermocellum. Nataf Y, Yaron S, Stahl F, Lamed R, Bayer EA, Scheper TH, Sonenshein AL, Shoham Y, J Bacteriol 2009 191 203 209 10.1128/JB.01190-08 18952792
47. ATP-binding cassette transporters in bacteria. Davidson AL, Chen J, Annu Rev Biochem 2004 73 241 268 10.1146/annurev.biochem.73.011303.073626 15189142
48. Sugar transport in Sulfolobus solfataricus is mediated by two families of binding protein-dependent ABC transporters. Elferink MG, Albers SV, Konings WN, Driessen AJ, Mol Microbiol 2001 39 1494 1503 10.1046/j.1365-2958.2001.02336.x 11260467
49. Two-component signal transduction as a target for microbial anti-infective therapy. Barrett JF, Hoch JA, Antimicrob Agents Ch 1998 42 1529 1536
50. A two-component system plays an important role in the root-colonizing ability of Pseudomonas fluorescens strain WCS365. Dekkers LC, Bloemendaal CJP, de Weger LA, Wijffelman CA, Spaink HP, Lugtenberg BJ, Mol Plant Microbe Interact 1998 11 45 56 10.1094/MPMI.1998.11.1.45 9425686
51. Root exudation of phytochemicals in Arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions. Chaparro JM, Badri DV, Bakker MG, Sugiyama A, Manter DK, Vivanco JM, PLoS ONE 2013 8 55731 10.1371/journal.pone.0055731 23383346
52. Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere. Trivedi P, He Z, Van Nostrand JD, Albrigo G, Zhou J, Wang N, The ISME Journal 2012 6 363 383 10.1038/ismej.2011.100 21796220
53. Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions. Schneider T, Keiblinger KM, Schmid E, Sterflinger-Gleixner K, Ellersdorfer G, Roschitzki B, Richter A, Eberl L, Zechmeister-Boltenstern S, Riedel K, ISME J 2012 6 1749 1762 10.1038/ismej.2012.11 22402400
54. Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities. Hettich RL, Sharma R, Chourey K, Giannone RJ, Curr Opin Microbiol 2012 15 373 380 10.1016/j.mib.2012.04.008 22632760
55. Metaproteomics: Harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. Hettich RL, Pan C, Chourey K, Giannone RJ, Anal Chem 2013 85 4203 4214 10.1021/ac303053e
56. Soil metaproteomics-Comparative evaluation of protein extraction protocols. Keiblinger KM, Wilhartitz IC, Schneider T, Roschitzki B, Schmid E, Eberl L, Riedel K, Zechmeister-Boltenstern S, Soil Biol Biochem 2012 54 14 24 23125465
57. Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. Erickson AR, Cantarel BL, Lamendella R, Darzi Y, Mongodin EF, Pan C, Shah M, Halfvarson J, Tysk C, Henrissat B, Raes J, Verberkmoes NC, Fraser CM, Hettich RL, Jansson JK, PLoS ONE 2012 7 49138 10.1371/journal.pone.0049138 23209564
58. Chen RK, Lin YQ, Zhang YB, Sun ZC, One hundred questions for sugarcane technique Beijing: China Agriculture Press 2009
59. Microbial and enzyme properties of apple orchard soil as affected by long-term application of copper fungicide. Wang QY, Zhou DM, Cang L, Soil Biol Biochem 2009 41 1504 1509 10.1016/j.soilbio.2009.04.010
60. Enzyme activities in apple orchard agroecosystems: How are they affected by management strategy and soil properties. Carine F, Capowiez Y, Stéven C, Soil Biol Biochem 2009 41 61 68 10.1016/j.soilbio.2008.09.018
61. Enhanced dissipation of PAHs from soil using mycorrhizal ryegrass and PAH-degrading bacteria. Yu XZ, Wu SC, Wu FY, Wong MH, J Hazard Mater 2011 186 1206 1217 10.1016/j.jhazmat.2010.11.116 21176862
62. Impact of allelopathic rice seedlings on rhizospheric microbial populations and their functional diversity. Lin RY, Rong H, Zhou JJ, Yu CP, Ye CY, Chen LS, Lin WX, Acta Ecologica Sinica 2007 27 3644 3654 10.1016/S1872-2032(07)60078-X
63. Comparison of two kinds of Biolog microplates (GN and ECO) in their ability to distinguish among aquatic microbial communities. Choi KH, Dobbs FC, J Microbiol Meth 1999 36 203 213 10.1016/S0167-7012(99)00034-2
64. Improved silver staining of plant proteins, RNA and DNA in polyacrylamide gels. Blum H, Beiers H, Gross HJ, Electrophoresis 1987 8 93 99 10.1002/elps.1150080203
65. Uniprot Database. http://www.uniprot.org
66. WEGO-Web Gene Ontology Annotation Plotting. http://wego.genomics.org.cn/ cgi-bin/wego/index.pl
67. WEGO: a web tool for plotting GO annotations. Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J, Nucleic Acids Res 2006 34 293 297 10.1093/nar/gkl031
68. KEGG-Kyoto Encyclopedia of Genes and Genomes http://www.genome.jp/kegg