Ecological Research

, Volume 33, Issue 4, pp 811–821 | Cite as

Improvement of Ni phytoextraction by Alyssum murale and its rhizosphere microbial activities by applying nitrogen fertilizer

  • Ali KansoEmail author
  • Sabine Azoury
  • Emile Benizri
  • Ahmad Kobaissi
  • Guillaume Echevarria
  • Catherine Sirguey
Special Feature Ultramafic Ecosystems: Proceedings of the 9th International Conference on Serpentine Ecology


Phytoextraction represents an innovative approach in the management of nickel (Ni) rich soils whether natural (ultramafic) or anthropogenic (contaminated sites). However, its success depends both on the production of a high plant biomass and the ability of plants to accumulate metals. The application of nitrogen (N) fertilizer can improve the biological and chemical soil fertility and thus agricultural yields. Moreover, soil microorganisms play a key role by influencing nutrient flows, which are the main limiting factors of plant growth in degraded soils. In this work, we investigated the effects of two levels of both Ni and mineral N soil applications on the microbial activities and Ni phytoextraction efficiency by Alyssum murale growing in a pot experiment during 5 months. Plant growth, nutrients and Ni uptake, soil microbial populations and their enzymatic activities involved in the biogeochemical cycles of nitrogen, phosphorus, carbon and sulfur (urease, alkaline phosphatase, β-glucosidase and arylsulfatase, respectively) were determined. The results showed that plant dry mass was unsurprisingly not affected when the soil Ni concentration was increased. However, it led to an increase of the amount of Ni extracted per pot. A negative effect of Ni addition was observed on both total bacteria and urease activity, without any effect on other enzymes. On the contrary, N fertilizer played a significant positive role by promoting both plant growth and Ni phytoextraction, partly as a result of the stimulation and flourishing of bacterial populations.


Nickel Hyperaccumulator Agromining Bacterial community Microbial enzymatic activities 



We express our deep appreciation to the research grant programs of the Lebanese University and the Lebanese Council for Scientific Research, which provided funding for this project. We are also thankful to the French National Research Agency for their support through the national Investissements d’avenir program, reference ANR-10-LABX-21-LABEX RESSOURCES21 and through the ANR-14-CE04-0005 project Agromine. Finally, we are grateful to the technical team of Laboratoire Sols et Environnement and PRASE—Lebanese University for their help and support.

Supplementary material

11284_2018_1630_MOESM1_ESM.pdf (374 kb)
Supplementary material 1 (PDF 374 kb)


  1. Abou Shanab RA, Angle JS, Delorme TA, Chaney RL, Van Berkum P, Moawad H, Ghanem K, Ghozlan HA (2003) Rhizobacterial effects on nickel extraction from soil and uptake by Alyssum murale. New Phytol 158:219–224. CrossRefGoogle Scholar
  2. Ajwa HA, Dell CJ, Rice CW, Rice CW (1999) Changes in enzyme activities and microbial biomass of tallgrass prairie soil as related to burning and nitrogen fertilization. Soil Biol Biochem 31:769–777. CrossRefGoogle Scholar
  3. Álvarez-López V, Prieto-Fernández Á, Cabello-Conejo MI, Kidd PS (2016) Organic amendments for improving biomass production and metal yield of Ni-hyperaccumulating plants. Sci Total Environ 548–549:370–379. CrossRefPubMedGoogle Scholar
  4. Bani A, Echevarria G, Sulçe S, Morel JL, Mullai A (2007) In-situ phytoextraction of Ni by a native population of Alyssum murale on an ultramafic site (Albania). Plant Soil 293:79–89. CrossRefGoogle Scholar
  5. Bani A, Pavlova D, Echevarria G, Mullaj A, Reeves RD, Morel JL, Sulçe S (2010) Nickel hyperaccumulation by the species of Alyssum and Thlaspi (Brassicaceae) from the ultramafic soils of the Balkans. Bot Serbica 34:3–14Google Scholar
  6. Bani A, Echevarria G, Sulçe S, Morel JL (2015) Improving the agronomy of Alyssum murale for extensive phytomining: a five-year field study. Int J Phytoremediation 17:117–127. CrossRefPubMedGoogle Scholar
  7. Baudoin E, Benizri E, Guckert A (2003) Impact of artificial root exudates on the bacterial community structure in bulk soil and maize rhizosphere. Soil Biol Biochem 35:1183–1192. CrossRefGoogle Scholar
  8. Bending GD, Turner MK, Rayns F, Marx MC, Wood M (2004) Microbial and biochemical soil quality indicators and their potential for differentiating areas under contrasting agricultural management regimes. Soil Biol Biochem 36:1785–1792. CrossRefGoogle Scholar
  9. Benizri E, Kidd P (2018) The role of the rhizosphere and microbes associated with hyperaccumulator plants in metal accumulation. In: Van der Ent A, Echevarria G, Baker A, Morel JL (eds) Agromining: farming for metals—extracting unconventional resources using plants. Springer Nature AG, Cham, pp 157–188CrossRefGoogle Scholar
  10. Biney C, Amuzu AT, Calamari D, Kaba N, Mbome IL, Naeve H, Ochumba PB, Osibanjo O, Radegonde V, Saad MA (1994) Review of heavy metals in the African aquatic environment. Ecotoxicol Environ Saf 28:134–159. CrossRefPubMedGoogle Scholar
  11. Boyd RS, Jaffré T (2009) Elemental concentrations of eleven new caledonian plant species from serpentine soils: elemental correlations and leaf-age effects. Northeast Nat 16:93–110CrossRefGoogle Scholar
  12. Caldwell BA (2005) Enzyme activities as a component of soil biodiversity: a review. Pedobiologia 49:637–644. CrossRefGoogle Scholar
  13. Chaney RL, Angle JS, Broadhurst CL, Peters CA, Tappero RV, Sparks DL (2007) Improved understanding of hyperaccumulation yields commercial phytoextraction and phytomining technologies. J Environ Qual 36:1429–1443. CrossRefPubMedGoogle Scholar
  14. Chaney RL, Chen KY, Li YM, Angle JS, Baker AJ (2008) Effects of calcium on nickel tolerance and accumulation in Alyssum species and cabbage grown in nutrient solution. Plant Soil 311:131–140. CrossRefGoogle Scholar
  15. Cunningham SD, Ow DW (1996) Promises and prospects of phytoremediation. Plant Physiol 110:715–719CrossRefPubMedPubMedCentralGoogle Scholar
  16. Deng Y, He Z, Xu M, Qin Y, Van Nostrand JD, Wu L, Roe BA, Wiley G, Hobbie SE, Reich PB, Zhou J (2012) Elevated carbon dioxide alters the structure of soil microbial communities. Appl Environ Microbiol 78:2991–2995. CrossRefPubMedPubMedCentralGoogle Scholar
  17. do Nascimento CWA, Xing B (2006) Phytoextraction: a review on enhanced metal availability and plant accumulation. Sci Agric 63:299–311. CrossRefGoogle Scholar
  18. Duineveld BM, Kowalchuk GA, Keijzer A, van Elsas JD, van Veen JA (2001) Analysis of bacterial communities in the rhizosphere of chrysanthemum via denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA as well as DNA fragments coding for 16S rRNA. Appl Environ Microbiol 67:172–178. CrossRefPubMedPubMedCentralGoogle Scholar
  19. Durand A, Piutti S, Rue M, Morel JL, Echevarria G, Benizri E (2016) Improving nickel phytoextraction by co-cropping hyperaccumulator plants inoculated by plant growth promoting rhizobacteria. Plant Soil 399:179–192. CrossRefGoogle Scholar
  20. Egamberdieva D, Kucharova Z, Davranov K, Berg G, Makarova N, Azarova T, Chebotar V, Tikhonovich I, Kamilova F, Validov SZ, Lugtenberg B (2011) Bacteria able to control foot and root rot and to promote growth of cucumber in salinated soils. Biol Fertil Soils 47:197–205. CrossRefGoogle Scholar
  21. Epelde L, Becerril JM, Alkorta I, Garbisu C (2009) Heavy metal phytoremediation: Microbial indicators of soil health for the assessment of remediation efficiency. Advances in applied bioremediation. Springer, Berlin, pp 299–313CrossRefGoogle Scholar
  22. García C, Roldán A, Hernández T (2005) Ability of different plant species to promote microbiological processes in semiarid soil. Geoderma 124:193–202. CrossRefGoogle Scholar
  23. Geisseler D, Scow KM (2014) Long-term effects of mineral fertilizers on soil microorganisms—a review. Soil Biol Biochem 75:54–63. CrossRefGoogle Scholar
  24. Glick BR (2010) Using soil bacteria to facilitate phytoremediation. Biotechnol Adv 28:367–374. CrossRefPubMedGoogle Scholar
  25. Guan G, Tu S, Yang J, Zhang J, Yang L (2011) A field study on effects of nitrogen fertilization modes on nutrient uptake, crop yield and soil biological properties in rice-wheat rotation system. Agric Sci China 10:1254–1261. CrossRefGoogle Scholar
  26. Hagmann J, Becker C, Müller J, Stegle O, Meyer RC, Wang G, Schneeberger K, Fitz J, Altmann T, Bergelson J, Borgwardt K (2015) Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage. PLoS Genet 11:e1004920. CrossRefPubMedPubMedCentralGoogle Scholar
  27. Hemida SK, Omar SA, Abdel-Mallek AY (1997) Microbial populations and enzyme activity in soil treated with heavy metals. Water Air Soil Pollut 95:13–22. CrossRefGoogle Scholar
  28. Hinsinger P, Plassard C, Jaillard B (2006) Rhizosphere: a new frontier for soil biogeochemistry. J Geochem Explor 88:210–213. CrossRefGoogle Scholar
  29. Jinghua X, Jiangming M, Jiong L (2005) Effects of nitrogen deposition on soil microorganism. Ecol Environ 14:777–782Google Scholar
  30. Kandeler E, Tscherko D, Bruce KD, Stemmer M, Hobbs PJ, Bardgett RD, Amelung W (2000) Structure and function of the soil microbial community in microhabitats of a heavy metal polluted soil. Biol Fertil Soils 32:390–400. CrossRefGoogle Scholar
  31. Khan AG (2005) Role of soil microbes in the rhizospheres of plants growing on trace metal contaminated soils in phytoremediation. J Trace Elem Med Biol 18:355–364. CrossRefPubMedGoogle Scholar
  32. Kibblewhite M, Ritz K, Swift M (2008) Soil health in agricultural systems. Philos Trans R Soc B Biol Sci 363:685–701. CrossRefGoogle Scholar
  33. Kidd PS, Álvarez-López V, Becerra-Castro C, Cabello-Conejo M, Prieto-Fernández Á (2017) Chapter three—potential role of plant-associated bacteria in plant metal uptake and implications in phytotechnologies. In: Cuypers A, Vangronsveld J (eds) Advances in botanical research. Academic Press, Cambridge, pp 87–126Google Scholar
  34. Klimek B (2012) Effect of long-term zinc pollution on soil microbial community resistance to repeated contamination. Bull Environ Contam Toxicol 88:617–622. CrossRefPubMedPubMedCentralGoogle Scholar
  35. Krumins JA, Goodey NM, Gallagher F (2015) Plant–soil interactions in metal contaminated soils. Soil Biol Biochem 80:224–231. CrossRefGoogle Scholar
  36. Lasat MM (2002) Phytoextraction of toxic metals: a review of biological mechanisms. J Environ Qual 31:109–120CrossRefPubMedGoogle Scholar
  37. Li YT, Rouland C, Benedetti M, Li FB, Pando A, Lavelle P, Dai J (2009) Microbial biomass, enzyme and mineralization activity in relation to soil organic C, N and P turnover influenced by acid metal stress. Soil Biol Biochem 41:969–977. CrossRefGoogle Scholar
  38. Liu W, Zhang C, Hu P, Luo Y, Wu L, Sale P, Tang C (2016) Influence of nitrogen form on the phytoextraction of cadmium by a newly discovered hyperaccumulator Carpobrotus rossii. Environ Sci Pollut Res Int 23:1246–1253. CrossRefPubMedGoogle Scholar
  39. Lopez S, Piutti S, Vallance J, Morel JL, Echevarria G, Benizri É (2017) Nickel drives bacterial community diversity in the rhizosphere of the hyperaccumulator Alyssum murale. Soil Biol Biochem 114:121–130. CrossRefGoogle Scholar
  40. Ma Y, Rajkumar M, Freitas H (2009) Isolation and characterization of Ni mobilizing PGPB from serpentine soils and their potential in promoting plant growth and Ni accumulation by Brassica spp. Chemosphere 75:719–725. CrossRefPubMedGoogle Scholar
  41. McNear DH, Chaney RL, Sparks DL (2010) The hyperaccumulator Alyssum murale uses complexation with nitrogen and oxygen donor ligands for Ni transport and storage. Phytochemistry 71:188–200. CrossRefPubMedGoogle Scholar
  42. Monsant AC, Tang C, Baker AJM (2008) The effect of nitrogen form on rhizosphere soil pH and zinc phytoextraction by Thlaspi caerulescens. Chemosphere 73:635–642. CrossRefPubMedGoogle Scholar
  43. Naseby DC, Lynch JM (2002) Enzymes and microorganisms in the rhizosphere. Enzym Environ Act Ecol Appl Marcel Dekker N Y 109–123Google Scholar
  44. Pattnaik BK, Equeenuddin SM (2016) Potentially toxic metal contamination and enzyme activities in soil around chromite mines at Sukinda Ultramafic Complex, India. J Geochem Explor 168:127–136. CrossRefGoogle Scholar
  45. Pessoa-Filho M, Barreto CC, dos Reis Junior FB, Fragoso RR, Costa FS, de Carvalho Mendes I, de Andrade LR (2015) Microbiological functioning, diversity, and structure of bacterial communities in ultramafic soils from a tropical savanna. Antonie Van Leeuwenhoek 107:935–949. CrossRefPubMedGoogle Scholar
  46. Pulford ID, Watson C (2003) Phytoremediation of heavy metal-contaminated land by trees—a review. Environ Int 29:529–540. CrossRefPubMedGoogle Scholar
  47. Renella G, Mench M, Landi L, Nannipieri P (2005) Microbial activity and hydrolase synthesis in long-term Cd-contaminated soils. Soil Biol Biochem 37:133–139. CrossRefGoogle Scholar
  48. Saad R, Kobaissi A, Robin C et al (2016) Nitrogen fixation and growth of Lens culinaris as affected by nickel availability: a pre-requisite for optimization of agromining. Environ Exp Bot 131:1–9. CrossRefGoogle Scholar
  49. Saha S, Prakash V, Kundu S, Kumar N, Mina BL (2008) Soil enzymatic activity as affected by long term application of farm yard manure and mineral fertilizer under a rainfed soybean–wheat system in N-W Himalaya. Eur J Soil Biol 44:309–315CrossRefGoogle Scholar
  50. Schwartz C, Echevarria G, Morel JL (2003) Phytoextraction of cadmium with Thlaspi caerulescens. Plant Soil 249:27–35CrossRefGoogle Scholar
  51. Sinsabaugh RL, Lauber CL, Weintraub MN, Ahmed B, Allison SD, Crenshaw C, Contosta AR, Cusack D, Frey S, Gallo ME, Gartner TB (2008) Stoichiometry of soil enzyme activity at global scale. Ecol Lett 11:1252–1264. CrossRefPubMedGoogle Scholar
  52. Sirguey C, Schwartz C, Morel JL (2006) Response of Thlaspi caerulescens to nitrogen, phosphorus and sulfur fertilisation. Int J Phytoremediation 8:149–161. CrossRefGoogle Scholar
  53. Smalla K, Wieland G, Buchner A, Zock A, Parzy J, Kaiser S, Roskot N, Heuer H, Berg G (2001) Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol 67:4742–4751CrossRefPubMedPubMedCentralGoogle Scholar
  54. Sobolev D, Begonia MFT (2008) Effects of heavy metal contamination upon soil microbes: lead-induced changes in general and denitrifying microbial communities as evidenced by molecular markers. Int J Environ Res Public Health 5:450–456CrossRefPubMedPubMedCentralGoogle Scholar
  55. Sowerby A, Emmett B, Beier C, Tietema A, Penuelas J, Estiarte M, Van Meeteren MJ, Hughes S, Freeman C (2005) Microbial community changes in heathland soil communities along a geographical gradient: interaction with climate change manipulations. Soil Biol Biochem 37:1805–1813. CrossRefGoogle Scholar
  56. Tabatabai MA, Bremner JM (1972) Assay of urease activity in soils. Soil Biol Biochem 4:479–487. CrossRefGoogle Scholar
  57. Tandy S, Healey JR, Nason MA, Williamson JC, Jones DL (2009) Heavy metal fractionation during the co-composting of biosolids, deinking paper fibre and green waste. Bioresour Technol 100:4220–4226. CrossRefPubMedGoogle Scholar
  58. Treseder KK (2008) Nitrogen additions and microbial biomass: a meta-analysis of ecosystem studies. Ecol Lett 11:1111–1120. CrossRefPubMedGoogle Scholar
  59. Tumi AF, Mihailović N, Gajić BA, Niketić M, Tomović G (2012) Comparative study of hyperaccumulation of nickel by Alyssum murale sl populations from the ultramafics of Serbia. Pol J Environ Stud 21:1855–1866Google Scholar
  60. van der Ent A, Baker AJ, Reeves RD, Pollard AJ, Schat H (2013) Hyperaccumulators of metal and metalloid trace elements: facts and fiction. Plant Soil 362:319–334. CrossRefGoogle Scholar
  61. Vangronsveld J, Herzig R, Weyens N, Boulet J, Adriaensen K, Ruttens A, Thewys T, Vassilev A, Meers E, Nehnevajova E, van der Lelie D (2009) Phytoremediation of contaminated soils and groundwater: lessons from the field. Environ Sci Pollut Res Int 16:765–794. CrossRefPubMedGoogle Scholar
  62. Vásquez-Murrieta MS, Migueles-Garduño I, Franco-Hernández O, Govaerts B, Dendooven L (2006) C and N mineralization and microbial biomass in heavy-metal contaminated soil. Eur J Soil Biol 42:89–98. CrossRefGoogle Scholar
  63. Xiao L, Guan D, Peart MR, Chen Y, Li Q, Dai J (2017) The influence of bioavailable heavy metals and microbial parameters of soil on the metal accumulation in rice grain. Chemosphere 185:868–878. CrossRefPubMedGoogle Scholar
  64. Zhang J, Ai Z, Liang C, Wang G, Xue S (2017) Response of soil microbial communities and nitrogen thresholds of Bothriochloa ischaemum to short-term nitrogen addition on the Loess Plateau. Geoderma 308:112–119. CrossRefGoogle Scholar

Copyright information

© The Ecological Society of Japan 2018

Authors and Affiliations

  1. 1.Applied Plant Biotechnology Laboratory, Faculty of SciencesLebanese UniversityBeirutLebanon
  2. 2.Laboratoire Sols et EnvironnementUniversité de Lorraine, INRANancyFrance

Personalised recommendations