Skip to main content

Advertisement

Log in

A Greenhouse Assay on the Effect of Applied Urea Amount on the Rhizospheric Soil Bacterial Communities

  • Original Article
  • Published:
Indian Journal of Microbiology Aims and scope Submit manuscript

Abstract

The rhizospheric bacteria play key role in plant nutrition and growth promotion. The effects of increased nitrogen inputs on plant rhizospheric soils also have impacted on whole soil microbial communities. In this study, we analyzed the effects of applied nitrogen (urea) on rhizospheric bacterial composition and diversity in a greenhouse assay using the high-throughput sequencing technique. To explore the environmental factors driving the abundance, diversity and composition of soil bacterial communities, the relationship between soil variables and the bacterial communities were also analyzed using the mantel test as well as the redundancy analysis. The results revealed significant bacterial diversity changes at different amounts of applied urea, especially between the control treatment and the N fertilized treatments. Mantel tests showed that the bacterial communities were significantly correlated with the soil nitrate nitrogen, available nitrogen, soil pH, ammonium nitrogen and total organic carbon. The present study deepened the understanding about the rhizospheric soil microbial communities under different amounts of applied urea in greenhouse conditions, and our work revealed the environmental factors affecting the abundance, diversity and composition of rhizospheric bacterial communities.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Vitousek PM, Hättenschwiler S, Olander L, Allison S (2002) Nitrogen and nature. Ambio 31:97–101. doi:10.1579/0044-7447-31.2.97

    Article  PubMed  Google Scholar 

  2. Ramirez KS, Craine JM, Fierer N (2012) Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes. Glob Change Biol 18:1918–1927. doi:10.1111/j.1365-2486.2012.02639.x

    Article  Google Scholar 

  3. Shen W, Lin X, Shi W, Min J, Gao N, Zhang H, Yin R, He X (2010) Higher rates of nitrogen fertilization decrease soil enzyme activities, microbial functional diversity and nitrification capacity in a Chinese polytunnel greenhouse vegetable land. Plant Soil 337:137–150. doi:10.1007/s11104-010-0511-2

    Article  CAS  Google Scholar 

  4. Shen W, Lin X, Gao N, Zhang H, Yin R, Shi W, Duan Z (2008) Land use intensification affects soil microbial populations, functional diversity and related suppressiveness of cucumber Fusarium wilt in China’s Yangtze River Delta. Plant Soil 306:117–127. doi:10.1007/s11104-010-0511-2

    Article  CAS  Google Scholar 

  5. Jorquera MA, Martínez OA, Marileo LG, Acuña JJ, Saggar S, Mora ML (2013) Effect of nitrogen and phosphorus fertilization on the composition of rhizobacterial communities of two Chilean Andisol pastures. World J Microbiol Biotechnol 30:99–107. doi:10.1007/s11274-013-1427-9

    Article  PubMed  Google Scholar 

  6. Spalding RF, Exner ME (1993) Occurrence of nitrate in groundwater—a review. J Environ Qual 22:392–402. doi:10.2134/jeq1993.00472425002200030002x

    Article  CAS  Google Scholar 

  7. Caballero-Mellado J, Onofre-Lemus J, Estrada-de los Santos P, Martínez-Aguilar L (2007) The tomato rhizosphere, an environment rich in nitrogen-fixing Burkholderia species with capabilities of interest for agriculture and bioremediation. Appl Environ Microbiol 73:5308–5319. doi:10.1128/AEM.00324-07

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  8. Cocking EC (2003) Endophytic colonization of plant roots by nitrogen-fixing bacteria. Plant Soil 252:169–175. doi:10.1023/A:1024106605806

    Article  CAS  Google Scholar 

  9. Rodríguez H, Fraga R (1999) Phosphate solubilizing bacteria and their role in plant growth promotion. Biotechnol Adv 17:319–339. doi:10.1016/S0734-9750(99)00014-2

    Article  PubMed  Google Scholar 

  10. Basak B, Biswas D (2009) Influence of potassium solubilizing microorganism (Bacillus mucilaginosus) and waste mica on potassium uptake dynamics by sudan grass (Sorghum vulgare Pers.) grown under two Alfisols. Plant Soil 317:235–255. doi:10.1007/s11104-008-9805-z

    Article  CAS  Google Scholar 

  11. De Boer W, Wagenaar AM, Klein Gunnewiek PJ, Van Veen JA (2007) In vitro suppression of fungi caused by combinations of apparently non-antagonistic soil bacteria. FEMS Microbiol Ecol 59:177–185. doi:10.1111/j.1574-6941.2006.00197.x

    Article  PubMed  Google Scholar 

  12. Brahim B (2013) Bacteria for plant growth promotion and disease management. In: Dinesh K (ed) Bacteria in agrobiology: disease management, Chap. 2. Springer, Berlin, pp 15–47. doi:10.1007/978-3-642-33639-3_2

    Google Scholar 

  13. Oh YM, Kim M, Lee-Cruz L, Lai-Hoe A, Go R, Ainuddin N, Rahim RA, Shukor N, Adams JM (2012) Distinctive bacterial communities in the rhizoplane of four tropical tree species. Microb Ecol 64:1018–1027. doi:10.1007/s00248-012-0082-2

    Article  PubMed  Google Scholar 

  14. Osés SM, Diez AM, Melero B, Luning PA, Jaime I, Rovira J (2013) Characterization by culture-dependent and culture-independent methods of the bacterial population of suckling-lamb packaged in different atmospheres. Food Microbiol 36:216–222. doi:10.1016/j.fm.2013.05.005

    Article  PubMed  Google Scholar 

  15. Kakumanu ML, Cantrell CL, Williams MA (2013) Microbial community response to varying magnitudes of desiccation in soil: a test of the osmolyte accumulation hypothesis. Soil Biol Biochem 57:644–653. doi:10.1016/j.soilbio.2012.08.014

    Article  CAS  Google Scholar 

  16. Walker AW, Sanderson JD, Churcher C, Parkes GC, Hudspith BN, Rayment N, Brostoff J, Parkhill J, Dougan G, Petrovska L (2011) High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Mirobiol 11:7. doi:10.1186/1471-2180-11-7

    Article  Google Scholar 

  17. Tamaki H, Wright CL, Li X, Lin Q, Hwang C, Wang S, Thimmapuram J, Kamagata Y, Liu W (2011) Analysis of 16S rRNA amplicon sequencing options on the Roche/454 next-generation titanium sequencing platform. PLoS ONE 6:e25263. doi:10.1371/journal.pone.0025263

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  18. Li H, Ye D, Wang X, Settles ML, Wang J, Hao Z, Zhou L, Dong P, Jiang Y, Ma ZS (2014) Soil bacterial communities of different natural forest types in Northeast China. Plant Soil 383:203–216. doi:10.1007/s11104-014-2165-y

    Article  CAS  Google Scholar 

  19. Aviva H, Larissa K, Mustafa G, Emine EK (1984) Rates of decomposition of plant residues and available nitrogen in soil, related to residue composition through simulation of carbon and nitrogen turnover. Soil Biol Biochem 36:255–266. doi:10.1016/j.soilbio.2003.09.012

    Google Scholar 

  20. Bremner J, Keeney D (1966) Determination and isotope-ratio analysis of different forms of nitrogen in soils: 3. Exchangeable ammonium, nitrate, and nitrite by extraction-distillation methods. Soil Sci Soc Am J 30:577–582. doi:10.2136/sssaj1966.03615995003000050015x

    Article  CAS  Google Scholar 

  21. Fernanda C, Hernán EE, Luis AA (2007) Soil available phosphorus status determines indigenous mycorrhizal colonization of field and glasshouse-grown spring wheat from Argentina. Appl Soil Ecol 35:1–9. doi:10.1016/j.apsoil.2006.06.001

    Article  Google Scholar 

  22. Peiffer JA, Spor A, Koren O, Jin Z, Tringe SG, Dangl JL, Buckler ES, Ley RE (2013) Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci USA 110:6548–6553. doi:10.1073/pnas.1302837110

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  23. Magoč T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957–2963. doi:10.1093/bioinformatics/btr507

    Article  PubMed Central  PubMed  Google Scholar 

  24. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336. doi:10.1038/nmeth.f.303

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  25. Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996–998. doi:10.1038/nmeth.2604

    Article  CAS  PubMed  Google Scholar 

  26. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267. doi:10.1128/AEM.00062-07

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  27. Ter Braak C, Smilauer P (1998) CANOCO reference manual and User’s guide to Canoco for windows: software for canonical community ordination (version 4.5)) Cajo JF ter Braak and Petr Smilauer. Centre for Biometry, Wageningen University, Netherlands

    Google Scholar 

  28. Qiu M, Zhang R, Xue C, Zhang S, Li S, Zhang N, Shen Q (2012) Application of bio-organic fertilizer can control Fusarium wilt of cucumber plants by regulating microbial community of rhizosphere soil. Biol Fertil Soils 48:807–816. doi:10.1007/s00374-012-0675-4

    Article  CAS  Google Scholar 

  29. Yang S, Wen X, Jin H, Wu Q (2012) Pyrosequencing investigation into the bacterial community in permafrost soils along the China-Russia Crude Oil Pipeline (CRCOP). PLoS ONE 7:e52730. doi:10.1371/journal.pone.0052730

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  30. Kersters K, De Vos P, Gillis M, Swings J, Vandamme P, Stackebrandt E (2006) Introduction to the Proteobacteria. In: Martin D (ed) The prokaryotes, vol 5., Proteobacteria: Alpha and Beta SubclassesSpringer, New York, pp 3–37. doi:10.1007/0-387-30745-1_2

    Chapter  Google Scholar 

  31. Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103:626–631. doi:10.1073/pnas.0507535103

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  32. Pernes-Debuyser A, Tessier D (2004) Soil physical properties affected by long-term fertilization. Eur J Soil Sci 55:505–512. doi:10.1111/j.1365-2389.2004.00614.x

    Article  CAS  Google Scholar 

  33. He JZ, Shen JP, Zhang LM, Zhu YG, Zheng YM, Xu MG, Di H (2007) Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environ Microbiol 9:2364–2374

    Article  CAS  PubMed  Google Scholar 

  34. Shen X-Y, Zhang L-M, Shen J-P, Li L-H, Yuan C-L, He J-Z (2011) Nitrogen loading levels affect abundance and composition of soil ammonia oxidizing prokaryotes in semiarid temperate grassland. J Soil Sediment 11:1243–1252. doi:10.1007/s11368-011-0375-y

    Article  CAS  Google Scholar 

  35. Rodrigo M, Paolina G, Jos MR (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 37:634–663. doi:10.1111/1574-6976.12028

    Article  Google Scholar 

Download references

Acknowledgments

This work was supported by the Program of the National Science Foundation of China (41171192).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Yanli Yi.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 142 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Shang, S., Yi, Y. A Greenhouse Assay on the Effect of Applied Urea Amount on the Rhizospheric Soil Bacterial Communities. Indian J Microbiol 55, 406–414 (2015). https://doi.org/10.1007/s12088-015-0551-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12088-015-0551-7

Keywords

Navigation