Plant and Soil

, Volume 330, Issue 1–2, pp 207–214 | Cite as

GEOCHEM-EZ: a chemical speciation program with greater power and flexibility

  • Jon E. Shaff
  • Benjamin A. Schultz
  • Eric J. Craft
  • Randy T. Clark
  • Leon V. Kochian
Regular Article


GEOCHEM-EZ is a multi-functional chemical speciation program, designed to replace GEOCHEM-PC, which can only be used on DOS consoles. Chemical speciation programs, such as GEOCHEM and GEOCHEM-PC, have been excellent tools for scientists designing appropriate solutions for their experiments. GEOCHEM-PC is widely used in plant nutrition and soil and environmental chemistry research to perform equilibrium speciation computations, allowing the user to estimate solution ion activities and to consider simple complexes and solid phases. As helpful as GEOCHEM-PC has been to scientists, the consensus was that the program was not very user friendly, was difficult to learn and to troubleshoot, and suffered from several functional weaknesses. To enhance the usability and to address the problems found in GEOCHEM-PC, we upgraded the program with a Java graphical interface, added Help files, and improved its power and function, allowing it to run on any computer that supports Windows XP, Vista or Windows 7.


Chemical speciation Nutrient solution Computer software Plant nutrition Ion activity 



Ethylenediaminetetraacetic acid





The authors would like to thank Dr. David Parker (University of California, Riverside) for his encouragement to improve the Geochem-PC program and for his helpful discussions. We gratefully acknowledge Dr. Wendell Norvell for providing Geochem and Geochem-PC background materials. Also, we want to sincerely thank Adam Famoso (Cornell University, Department of Plant Breeding) and Michael Rutzke (USDA-ARS, R.W. Holley Center) for all of their work on the ICP-ES analysis of the Yoshida’s rice nutrient solution.


  1. Diatloff E, Asher CJ, Smith FW (1993) Use of Geochem-PC to predict rare earth element (REE) in nutrient solutions. Plant Soil 155(156):251–254CrossRefGoogle Scholar
  2. Farrell RE, Germida JJ, Huang PM (1993) Effects of chemical speciation in growth media on the toxicity of mercury (II). Appl Environ Microbiol 59:1507–1514PubMedGoogle Scholar
  3. Fox TC, Shaff JE, Grusak MA, Norvell WA, Chen Y, Chaney RL, Kochian LV (1996) Direct measurement of 59Fe-labeled Fe2+ influx in roots of pea using chelator buffer system to control free Fe2+ in solution. Plant Physiol 111:93–100PubMedGoogle Scholar
  4. Hacisalihoglu G, Hart JJ, Vallejos CE, Kochian LV (2004) The role of shoot-localized processes in the mechanism of Zn efficiency in common bean. Planta 218:704–711CrossRefPubMedGoogle Scholar
  5. Liao H, Wan H, Shaff J, Wang X, Yan X, Kochian LV (2006) Phosphorous and aluminum interactions in soybean in relation to aluminum tolerance. Exudation of specific organic acids from different regions of the intact root system. Plant Physiol 141:674–684CrossRefPubMedGoogle Scholar
  6. Nguyen BD, Brar DS, Buu CB, Nguyen TV, Pham LN, Nguyen HT (2003) Identification and mapping of the QTL for aluminum tolerance introgressed from the new source, ORYZA RUFIPOGON Griff., into indica rice (Oryza sativa L.). Theor Appl Genet 106:583–593PubMedGoogle Scholar
  7. Parker DR, Zelazny LW, Kinraide TB (1987) Improvements to the program Geochem. Soil Sci Soc Am J 51:488–491Google Scholar
  8. Parker DR, Norvell WA, Chaney RL (1995a) GEOCHEM-PC: a chemical speciation program for IBM and compatible personal computers. In: Loeppert RH et al (eds) Chemical equilibrium and reaction models. Soil Science Society of America, Special Publication 42, Madison, pp 253–269Google Scholar
  9. Parker DR, Norvell WA, Chaney RL (1995b) Chemical equilibrium models: applications to plant nutrition research. In: Loeppert RH et al (eds) Chemical equilibrium and reaction models. Soil Science Society of America, Special Publication 42, Madison, pp 163–200Google Scholar
  10. Parker DR, Pedler JF, Ahnstrom ZA, Resketo M (2001) Reevaluating the free-ion activity model of trace metal toxicity toward higher plants: experimental evidence with copper and zinc. Environ Toxicol Chem 20:899–906PubMedCrossRefGoogle Scholar
  11. Ritchie JM, Cresser M, Cotter-Howells J (2001) Toxicological response of a bioluminescent microbial assay to Zn, Pb, and Cu in artificial soil solution: relationship with total metal concentrations and free ion activities. Environ Pollut 114:129–136CrossRefPubMedGoogle Scholar
  12. Schmidke I, Krüger C, Frömmichen R, Scholz G, Stephan UW (1999) Phloem loading and transport characteristics of iron in interaction with plant-endogenous ligands in castor bean seedlings. Physiol Plant 106:82–89CrossRefGoogle Scholar
  13. Shen R, Iwashita T, Ma JF (2004) Form of Al changes with Al concentration in leaves of buckwheat. J Exp Bot 55:131–136CrossRefPubMedGoogle Scholar
  14. Shenker M, Hadar Y, Chen Y (1999) Kinetics of iron complexing and metal exchange in solutions by rhizoferrin, a fungal siderophore. Soil Sci Soc Am J 63:1681–1687Google Scholar
  15. Silva IR, Smyth TJ, Israel DW, Raper CD, Rufty TW (2001) Magnesium is more efficient than calcium in alleviating aluminum rhizotoxicity in soybean and ameliorative effect is not explained by the Gouy-Chapman-Stern model. Plant Cell Physiol 42:538–545CrossRefPubMedGoogle Scholar
  16. Sposito G, Mattigod SV (1980) Geochem: a computer program for the calculation of chemical equilibria in soil solution and other natural water systems. Kearney Found. Soil Sci, Univ of California, RiversideGoogle Scholar
  17. Taylor GJ, McDonald-Stephens JL, Hunter DB, Bertsch PM, Elmore D, Rengel Z, Reid R (2000) Direct measurement of aluminum uptake and distribution in single cells of Chara corallina. Plant Physiol 123:987–996CrossRefPubMedGoogle Scholar
  18. Trostle CL, Bloom PR, Allan DL (2001) HEDTA-Nitriloacetic acid chelator-buffered nutrient solution for zinc deficiency evaluation in rice. Soil Sci Soc Am J 65:385–390Google Scholar
  19. Vassil AD, Kapulnik Y, Raskin I, Salt DE (1998) The role of EDTA in lead transport and accumulation by Indian Mustard. Plant Physiol 117:447–453CrossRefPubMedGoogle Scholar
  20. Wu P, Liao CY, Hu B, Yi KK, Jin WZ, Ni JJ, He C (2000) QTLs and epistasis for aluminum tolerance in rice (Oryza sativa L.) at different seedling stages. Theor Appl Genet 100:1295–1303CrossRefGoogle Scholar
  21. Yoshida S, Forno DA, Cock YH, Gomez KA (1971) Laboratory manual for physiological studies of rice, 2nd edn. International Rice research Institute, Los Baños, pp 53–57Google Scholar

Copyright information

© US Government 2009

Authors and Affiliations

  • Jon E. Shaff
    • 1
    • 2
  • Benjamin A. Schultz
    • 1
    • 2
  • Eric J. Craft
    • 1
  • Randy T. Clark
    • 1
    • 3
  • Leon V. Kochian
    • 1
  1. 1.Robert W. Holley Center for Agriculture and Health, USDA-ARSCornell UniversityIthacaUSA
  2. 2.Department of Plant BiologyCornell UniversityIthacaUSA
  3. 3.Department of Biological and Environmental EngineeringCornell UniversityIthacaUSA

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