Metagenomic analysis of the rhizosphere soil microbiome with respect to phytic acid utilization

Microbes and Environments

Volumn 28, Issue 1, 2013, Pages 120-127

  Unno, Yusuke ^a   Shinano, Takuro ^a  

^a NATIONAL AGRICULTURAL RESEARCH CENTER FOR HOKKAIDO REGION   (Japan)

Author keywords

Inositol phosphates; Metagenome; Organic phosphorus; Pyrosequence

Indexed keywords

PHYTIC ACID; RNA 16S;

ARTICLE; BACTERIUM; CLASSIFICATION; DNA SEQUENCE; EURYARCHAEOTA; GENETICS; GROWTH, DEVELOPMENT AND AGING; LOTUS; METABOLISM; METAGENOME; METAGENOMICS; MICROBIOLOGY; PHYLOGENY; PLANT ROOT; RHIZOSPHERE; SOIL;

BACTERIA; EURYARCHAEOTA; LOTUS; METAGENOME; METAGENOMICS; PHYLOGENY; PHYTIC ACID; PLANT ROOTS; RHIZOSPHERE; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL; SOIL MICROBIOLOGY;

EID: 84875139098     PISSN: 13426311     EISSN: 13474405     Source Type: Journal    
DOI: 10.1264/jsme2.ME12181     Document Type: Article

References (56)

1. Adams, M.A., and J.S. Pate. 1992. Availability of organic and inorganic forms of phosphorus to lupins (Lupinus spp). Plant Soil. 145:107-113.
2. Anderson, G. 1980. Assessing organic phosphorus in soils, p. 411-432. In F.E. Khasawneh, E.C. Sample, and E.J. Kamprath (ed.), The Role of Phosphorus in Agriculture. American Society of Agronomy.
3. Barea, J.M., E. Navarro, and E. Montoya. 1976. Production of plant growth regulators by rhizosphere phosphatesolubilizing bacteria. J. Appl. Bacteriol. 40:129-134.
4. Beck, E., A. Fusseder, and M. Kraus. 1989. The maize root-system insitu-evaluation of structure and capability of utilization of phytate and inorganic soil phosphates. Z Pflanzen Bodenkunde. 152:159-167.
5. Bloemberg, G.V., and B.J.J. Lugtenberg. 2001. Molecular basis of plant growth promotion and biocontrol by rhizobacteria. Curr. Opin. Plant Biol. 4:343-350.
6. Cade-Menun, B.J., C.W. Liu, R. Nunlist, and J.G. McColl. 2002. Soil and litter phosphorus-31 nuclear magnetic resonance spectroscopy: Extractants, metals, and phosphorus relaxation times, p. 457-465. In Book Soil and Litter Phosphorus-31 Nuclear Magnetic Resonance Spectroscopy: Extractants, Metals, and Phosphorus Relaxation Times, vol. Amer. Soc. Agronomy.
7. Cade-Menun, B.J., and C.M. Preston. 1996. A comparison of soil extraction procedures for P-31 NMR spectroscopy. Soil Science. 161:770-785.
8. Chu, H.M., R.T. Guo, T.W. Lin, et al. 2004. Structures of Selenomonas ruminantium phytase in complex with persulfated phytate: DSP phytase fold and mechanism for sequential substrate hydrolysis. Structure. 2:2015-2024.
9. Cordell, D., J.O. Drangert, and S. White. 2009. The story of phosphorus: global food security and food for thought. Global Environmental Change-Human and Policy Dimensions 19:292-305.
10. Craxton, A., N. Ali, and S.B. Shears. 1995. Comparison of the activities of a multiple inositol polyphosphate phosphatase obtained from several sources-a search for heterogeneity in this enzyme. Biochem. J. 305:491-498.
11. Dick, G.J., S. Podell, H.A. Johnson, et al. 2008. Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1. Appl. Environ. Microbiol. 74:2646-2658.
12. Dox, A.W., and R. Golden. 1911. Phytase in lower fungi. J. Biol. Chem. 10:183-186.
13. Duineveld, B.M., G.A. Kowalchuk, A. Keijzer, J.D. van Elsas, and J.A. van Veen. 2001. Analysis of bacterial communities in the rhizosphere of chrysanthemum via denaturing gradient gel electro-phoresis of PCR-amplified 16S rRNA as well as DNA fragments coding for 16S rRNA. Appl. Environ. Microbiol. 67:172-178.
14. Edwards, R.A., B. Rodriguez-Brito, L. Wegley, et al. 2006. Using pyrosequencing to shed light on deep mine microbial ecology. Bmc Genomics 7:57-70.
15. Feng, G., Y.C. Song, X.L. Li, and P. Christie. 2003. Contribution of arbuscular mycorrhizal fungi to utilization of organic sources of phosphorus by red clover in a calcareous soil. Appl. Soil Ecol. 22:139-148.
16. Findenegg, G.R., and J.A. Nelemans. 1993. The effect of phytase on the availability of p from myoinositol hexaphosphate (phytate) for maize roots. Plant Soil. 154:189-196.
17. Giovannetti, M., and B. Mosse. 1980. Evaluation of techniques for measuring vesicular arbuscular mycorrhizal infection in roots. New Phytol. 84:489-500.
18. Hayes, J.E., A.E. Richardson, and R.J. Simpson. 2000. Components of organic phosphorus in soil extracts that are hydrolysed by phytase and acid phosphatase. Biol. Fert. Soils. 32:279-286.
19. Idriss, E.E., O. Makarewicz, A. Farouk, et al. 2002. Extracellular phytase activity of Bacillus amyloliquefaciens FZB45 contributes to its plant-growth-promoting effect. Microbiology 148:2097-2109.
20. Imaizumi-Anraku, H., M. Kawaguchi, H. Koiwa, S. Akao, and K. Syono. 1997. Two ineffective-nodulating mutants of Lotus japonicus-different phenotypes caused by the blockage of endocytotic bacterial release and nodule maturation. Plant Cell Physiol. 38:871-881.
21. Jorquera, M., O. Martínez, F. Maruyama, P. Marschner, and M.L. Mora. 2008. Current and future biotechnological applications of bacterial phytases and phytase-producing bacteria. Microbes Environ. 23:182-191.
22. Kloepper, J.W., J. Leong, M. Teintze, and M.N. Schroth. 1980. Enhanced plant growth by siderophores produced by plant growth-promoting rhizobacteria. Nature 268:885-886.
23. Krause, L., N.N. Diaz, R.A. Edwards, et al. 2008. Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor. J. Biotechnol. 136:91-101.
24. Kuske, C.R., K.L. Banton, D.L. Adorada, et al. 1998. Small-scale DNA sample preparation method for field PCR detection of microbial cells and spores in soil. Appl. Environ. Microbiol. 64:2463-2472.
25. Martin, J.K. 1973. The influence of rhizosphere microflora on the availability of 32P myo-inositol hexaphosphate phosphorus to wheat. Soil Biol. Biochem. 5:473-483.
26. Meyer, F., D. Paarmann, M. D'Souza, et al. 2008. The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. Bmc Bioinformatics 9:386-394.
27. Mullaney, E.J., and A.H.J. Ullah. 2003. The term phytase comprises several different classes of enzymes. Biochem. Biophys. Res. Commun. 312:179-184.
28. Murphy, J., and J.P. Riley. 1962. A modified single solution method for the determination of phosphate in natural waters. Anal. Chim. Acta. 27:31-36.
29. Muyzer, G., E.C. Dewaal, and A.G. Uitterlinden. 1993. Profiling of complex microbial-populations by denaturing gradient gel-electrophoresis analysis of polymerase chain reaction-amplified genes-coding for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
30. Omotoso, T.I., and A. Wild. 1970. Content of inositol phosphates in some English and Nigerian soils. J. Soil Sci. 21:216-223.
31. Parks, D.H., and R.G. Beiko. 2010. Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26:715-721.
32. Puhl, A.A., R. Greiner, and L.B. Selinger. 2009. Stereospecificity of myo-inositol hexakisphosphate hydrolysis by a protein tyrosine phosphatase-like inositol polyphosphatase from Megasphaera elsdenii. Appl. Microbiol. Biotechnol. 82:95-103.
33. Richardson, A.E. 2001. Prospects for using soil microorganisms to improve the acquisition of phosphorus by plants. Aust. J. Plant Physiol. 28:897-906.
34. Richardson, A.E., and P.A. Hadobas. 1997. Soil isolates of Pseudomonas spp. that utilize inositol phosphates. Can. J. Microbiol. 43:509-516.
35. Richardson, A.E., P.A. Hadobas, and J.E. Hayes. 2001. Extracellular secretion of Aspergillus phytase from Arabidopsis roots enables plants to obtain phosphorus from phytate. Plant J. 25:641-649.
36. Richardson, A.E., P.A. Hadobas, J.E. Hayes, C.P. O'Hara, and R.J. Simpson. 2001. Utilization of phosphorus by pasture plants supplied with myo-inositol hexaphosphate is enhanced by the presence of soil micro-organisms. Plant Soil. 229:47-56.
37. Richardson, A.E., P.J. Hocking, R.J. Simpson, and T.S. George. 2009. Plant mechanisms to optimise access to soil phosphorus. Crop & Pasture Science. 60:124-143.
38. Sait, M., P. Hugenholtz, and P.H. Janssen. 2002. Cultivation of globally-distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ. Microbiol. 4:654-666.
39. Sato, S., and S. Tabata. 2006. Lotus japonicus as a platform for legume research. Curr. Opin. Plant Biol. 9:128-132.
40. Schlüter, A., T. Bekel, N.N. Diaz, et al. 2008. The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology. J. Biotechnol. 136:77-90.
41. Sommers, L.E., and D.W. Nelson. 1972. Determination of total phosphorus in soils: a rapid perchloric acid digestion procedure sommers and nelson. Soil Sci. Soc. Am. J. 36:902-904.
42. Steen, I. 1998. Phosphorus availability in the 21st century management of a non-renewable resource. Phosphorus and Potassium 217:25-31.
43. Suzuki, U., K. Yoshimura, and M. Takaishi. 1907. Uber ein Enzym "Phytase" das Anhydro-oxy-methylen-diphosphosaure spaltet. Bull. Coll. Agr. Tokyo Imper. Univ. 7:503-505.
44. Tarafdar, J.C., and N. Claassen. 1988. Organic phosphorus-compounds as a phosphorus source for higher-plants through the activity of phosphatases produced by plant-roots and microorganisms. Biol. Fert. Soils. 5:308-312.
45. Tettelin, H., V. Masignani, M.J. Cieslewicz, et al. 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc. Natl. Acad. Sci. U.S.A. 102:13950-13955.
46. Tringe, S.G., C. von Mering, A. Kobayashi, et al. 2005. Comparative metagenomics of microbial communities. Science 308:554-557.
47. Truog, E. 1930. The determination of the readily available phosphorus of soils. J. Am. Soc. Agron. 22:874-882.
48. Turner, B.L. 2005. Organic phosphorus transfer from terrestrial to aquatic environments, p. 269-294. In B.L. Turner, E. Frossard, and D.S. Baldwin (ed.), Organic Phosphorus in the Environment. CABI Publishing, Oxfordshire, UK.
49. Turner, B.L., N. Mahieu, and L.M. Condron. 2003. Quantification of myo-inositol hexakisphosphate in alkaline soil extracts by solution P31 NMR spectroscopy and spectral deconvolution. Soil Sci. 168:469-478.
50. Turner, B.L., S. Newman, A.W. Cheesman, and K.R. Reddy. 2007. Sample pretreatment and phosphorus speciation in wetland soils. Soil Sci. Soci. Ame. J. 71:1538-1546.
51. Tyson, G.W., J. Chapman, P. Hugenholtz, et al. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37-43.
52. Unno, Y., K. Okubo, J. Wasaki, T. Shinano, and M. Osaki. 2005. Plant growth promotion abilities and microscale bacterial dynamics in the rhizosphere of Lupin analysed by phytate utilization ability. Environ. Microbiol. 7:396-404.
53. Venter, J.C., K. Remington, J.F. Heidelberg, et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74.
54. Wang, X.R., Y.X. Wang, J. Tian, et al. 2009. Overexpressing AtPAP15 enhances phosphorus efficiency in soybean. Plant Physiol. 151:233-240.
55. Wegley, L., R. Edwards, B. Rodriguez-Brito, H. Liu, and F. Rohwer. 2007. Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ. Microbiol. 9:2707-2719.
56. Whipps, J.M. 1990. Carbon economy, p. 59-97. In J.M. Lynch. (ed.), The Rhizosphere. Wiley & Son, John Chichester, West Sussex, UK.