Characterization of Aspergillus niger siderophore that mediates bioleaching of rare earth elements from phosphorites

  • Yehia Osman
  • Ahmed Gebreil
  • Amr M. MowafyEmail author
  • Tarek I. Anan
  • Samar M. Hamed
Original Paper


Siderophores are extra-cellular inducible compounds produced by aerobic microorganisms and plants to overcome iron insolubility via its chelation and then uptake inside the cell. This work aims to study the characteristics of siderophore that is produced by a rhizosphere-inhabiting fungus. This fungus has been morphologically and molecularly identified as Aspergillus niger with the ability to produce 87% siderophore units. The obtained siderophore in PDB medium gave a positive result with tetrazolium test and a characteristic spectrum with a maximum absorbance at 450 nm in FeCl3 test that did not shift in response to different pH degrees (5–9). This indicates that the obtained siderophore is a trihydroxymate in nature. After purification, the FTIR and NMR analyses showed that the obtained siderophore is considered to be ferrichrome. The purified siderophore has been further evaluated as a tool to extract uranium, thorium and rare earth elements (REEs) from Egyptian phosphorites obtained from Abu Tartur Mine area. The inductively coupled plasma atomic emission spectroscopy analysis showed that the highest removal efficiency percentage was for uranium (69.5%), followed by samarium (66.7%), thorium (55%), lanthanum (51%), and cerium (50.1%). This result confirmed the ability of hydroxymate siderophores to chelate the aforementioned precious elements, a result that paves the way for bioleaching to replace abiotic techniques in order to save the cost of such elements in an environmentally friendly way.

Graphic abstract


Aspergillus niger Bioleaching Egyptian phosphorites Ferrichrome Hydroxymate siderophores Rare earth elements 



The authors thank Prof. Rania Zaky and Prof. Saad Shaaban, chemistry department, faculty of science, Mansoura University for interpretation of the FTIR and NMR data.


  1. Andres Y, Texier A-C, Le Cloirec P (2003) Rare earth elements removal by microbial biosorption: a review. Environ Technol 24:1367–1375CrossRefGoogle Scholar
  2. Arnow LE (1937) Colorimetric determination of the components of 3, 4-dihydroxyphenylalanine-tyrosine mixtures. J Biol Chem 118:531–537Google Scholar
  3. Baakza A, Vala A, Dave B, Dube H (2004) A comparative study of siderophore production by fungi from marine and terrestrial habitats. J Exp Mar Biol Ecol 311:1–9CrossRefGoogle Scholar
  4. Barmettler F, Castelberg C, Fabbri C, Brandl H (2016) Microbial mobilization of rare earth elements (REE) from mineral solids—a mini review. AIMS Microbiol 2:190–204CrossRefGoogle Scholar
  5. Barnett HL, Hunter BB (1998) Illustrated genera of imperfect fungi, edn 4. American Phytopathological Society (APS Press), St. PaulGoogle Scholar
  6. Briat J-F, Lobréaux S (1997) Iron transport and storage in plants. Trends Plant Sci 2:187–193CrossRefGoogle Scholar
  7. Brisson VL, Zhuang WQ, Alvarez-Cohen L (2016) Bioleaching of rare earth elements from monazite sand. Biotechnol Bioeng 113:339–348CrossRefGoogle Scholar
  8. Chattopadhyay P, Banerjee SK, Sen K, Chakrabarti P (1985) Lipid profiles of Aspergillus niger and its unsaturated fatty acid auxotroph, UFA2. Can J Microbiol 31:352–355CrossRefGoogle Scholar
  9. Christenson EA, Schijf J (2011) Stability of YREE complexes with the trihydroxamate siderophore desferrioxamine B at seawater ionic strength. Geochim Cosmochim Acta 75:7047–7062CrossRefGoogle Scholar
  10. Clark BL (2004) Characterization of a catechol-type siderophore and the detection of a possible outer membrane receptor protein from Rhizobium leguminosarum strain IARI 312. A M.Sc. thesis: presented to the faculty of the Department of Health Sciences East Tennessee State UniversityGoogle Scholar
  11. Crowley DE (2006) Microbial siderophores in the plant rhizosphere. Iron nutrition in plants and rhizospheric microorganisms. Springer, New York, pp 169–198CrossRefGoogle Scholar
  12. Dave B, Dube H (2000) Chemical characterization of fungal siderophores. Indian J Exp Biol 38:56–62PubMedGoogle Scholar
  13. Desouky OA, El-Mougith AA, Hassanien WA, Awadalla GS, Hussien SS (2016) Extraction of some strategic elements from thorium–uranium concentrate using bioproducts of Aspergillus ficuum and Pseudomonas aeruginosa. Arab J Chem 9:S795–S805CrossRefGoogle Scholar
  14. El-Anwar EAA (2018) Lithologic characterization of the phosphorite-bearing Duwi formation (Campanian). Carbonates Evaporites, South Esna. CrossRefGoogle Scholar
  15. Franken AC, Lechner BE, Werner ER, Haas H, Lokman BC, Ram AF, van den Hondel CA, de Weert S, Punt PJ (2014) Genome mining and functional genomics for siderophore production in Aspergillus niger. Brief Funct Genomics 13:482–492CrossRefGoogle Scholar
  16. Gholami RM, Borghei S, Mousavi S (2011) Fungal leaching of hazardous heavy metals from a spent hydrotreating catalyst. World Acad Sci, Eng Technol, Int J Chem, Mol, Nucl, Mater Metall Eng 5:362–367Google Scholar
  17. Gupta V, Saharan K, Kumar L, Gupta R, Sahai V, Mittal A (2008) Spectrophotometric ferric ion biosensor from Pseudomonas fluorescens culture. Biotechnol Bioeng 100:284–296CrossRefGoogle Scholar
  18. Haas H (2014) Fungal siderophore metabolism with a focus on Aspergillus fumigatus. Nat Prod Rep 31:1266–1276CrossRefGoogle Scholar
  19. Hussein KA, Joo JH (2014) Potential of siderophore production by bacteria isolated from heavy metal: polluted and rhizosphere soils. Curr Microbiol 68:717–723CrossRefGoogle Scholar
  20. Ismael I (2002) Rare earth elements in Egyptian phosphorites. Chin J Geochem. 21:19–28CrossRefGoogle Scholar
  21. Johnson DB (2006) Biohydrometallurgy and the environment: intimate and important interplay. Hydrometallurgy 83:153–166CrossRefGoogle Scholar
  22. Johnson L (2008) Iron and siderophores in fungal–host interactions. Mycol res. 112:170–183CrossRefGoogle Scholar
  23. Kejela T, Thakkar VR, Patel RR (2017) A novel strain of Pseudomonas inhibits Colletotrichum gloeosporioides and Fusarium oxysporum infections and promotes germination of coffee. Rhizosphere 4:9–15CrossRefGoogle Scholar
  24. Khamna S, Yokota A, Lumyong S (2009) Actinomycetes isolated from medicinal plant rhizosphere soils: diversity and screening of antifungal compounds, indole-3-acetic acid and siderophore production. World J Microbiol Biotechnol 25:649CrossRefGoogle Scholar
  25. Mendes R, Garbeva P, Raaijmakers JM (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 37:634–663CrossRefGoogle Scholar
  26. Meyer Ja, Abdallah M (1978) The fluorescent pigment of Pseudomonas fluorescens: biosynthesis, purification and physicochemical properties. Microbiology 107:319–328Google Scholar
  27. Milagres AM, Machuca A, Napoleao D (1999) Detection of siderophore production from several fungi and bacteria by a modification of chrome azurol S (CAS) agar plate assay. J Microbiol Methods 37:1–6CrossRefGoogle Scholar
  28. Mirabello SA (2006) Influence of siderophore producing bacteria and organic ligands on phase distribution of cadmium and its uptake by Brassica napus in the presence of goethite. Cornell University, New YorkGoogle Scholar
  29. Murugappan R, Aravinth A, Karthikeyan M (2011) Chemical and structural characterization of hydroxamate siderophore produced by marine Vibrio harveyi. J Ind Microbiol Biotechnol 38:265–273CrossRefGoogle Scholar
  30. Neilands JB (1981) Microbial iron compounds. Annu Rev Biochem 50:715–731CrossRefGoogle Scholar
  31. Neilands J (1995) Siderophores: structure and function of microbial iron transport compounds. J Biol Chem 270:26723–26726CrossRefGoogle Scholar
  32. Oide S, Moeder W, Krasnoff S, Gibson D, Haas H, Yoshioka K, Turgeon BG (2006) NPS6, encoding a nonribosomal peptide synthetase involved in siderophore-mediated iron metabolism, is a conserved virulence determinant of plant pathogenic ascomycetes. Plant Cell 18:2836–2853CrossRefGoogle Scholar
  33. Ozaki T, Suzuki Y, Nankawa T, Yoshida T, Ohnuki T, Kimura T, Francis AJ (2006) Interactions of rare earth elements with bacteria and organic ligands. J Alloys Compds 408:1334–1338CrossRefGoogle Scholar
  34. Patel D, Patel S, Thakar P, Saraf M (2017) Siderophore producing Aspergillus spp. as bioinoculant for enhanced growth of mung bean. Int J Adv Agric Sci Technol 6:111–120Google Scholar
  35. Rajkumar M, Ae N, Prasad MNV, Freitas H (2010) Potential of siderophore-producing bacteria for improving heavy metal phytoextraction. Trends Biotechnol 28:142–149CrossRefGoogle Scholar
  36. Sah S, Singh R (2015) Siderophore: structural and functional characterisation—a comprehensive review. Agriculture (Polnohospodárstvo) 61:97–114CrossRefGoogle Scholar
  37. Saha R, Saha N, Donofrio RS, Bestervelt LL (2013) Microbial siderophores: a mini review. J Basic Microbiol 53:303–317CrossRefGoogle Scholar
  38. Saha M, Sarkar S, Sarkar B, Sharma BK, Bhattacharjee S, Tribedi P (2016) Microbial siderophores and their potential applications: a review. Environ Sci Pollut R 23:3984–3999CrossRefGoogle Scholar
  39. Shenker M, Oliver I, Helmann M, Hadar Y, Chen Y (1992) Utilization by tomatoes of iron mediated by a siderophore produced by Rhizopus arrhizus. J Plant Nutr 15:2173–2182CrossRefGoogle Scholar
  40. Snow G (1954) Mycobactin. A growth factor for Mycobacterium johnei. Part II. Degradation, and identification of fragments. J Chem Soc (Resumed) 1954:2588–2596CrossRefGoogle Scholar
  41. Winkelmann G (1992) Structures and functions of fungal siderophores containing hydroxamate and complexone type iron binding ligands. Mycol Res 96:529–534CrossRefGoogle Scholar
  42. Wright WH IV (2010) Isolation and identification of the siderophore “vicibactin” produced by Rhizobium leguminosarum ATCC 14479. East Tennessee State University, Johnson CityGoogle Scholar
  43. Wright W, Little J, Liu F, Chakraborty R (2013) Isolation and structural identification of the trihydroxamate siderophore vicibactin and its degradative products from Rhizobium leguminosarum ATCC 14479 bv. trifolii. Biometals 26:271–283CrossRefGoogle Scholar
  44. Yadav J, Verma JP, Tiwari KN (2011) Plant growth promoting activities of fungi and their effect on chickpea plant growth. Asian J Biol Sci 4:291–299CrossRefGoogle Scholar
  45. Yeole R, Dave B, Dube H (2001) Siderophore production by fluorescent pseudomonads colonizing roots of certain crop plants.Google Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Botany Department, Faculty of ScienceMansoura UniversityMansouraEgypt
  2. 2.Geology Department, Faculty of ScienceMansoura UniversityMansouraEgypt

Personalised recommendations