Scientific literature review on nutrient monitoring

History on use of sentinel organisms to assess soil quality – farmers’ traditional knowledge

Human beings have a long history of agriculture.  The earliest evidence of farming is currently estimated to be 10,000 BC, where rye grains with characteristics indicative of domestication were identified in Abu Hureyra, Syria (Vasey, 1992).  The later four ancient civilizations that arose between 5000 – 1500 BC (Egypt, China, Mesopotamia and Indus civilizations) all evolved around great rivers that provided successful establishment due to agriculture, known to archeologists through detailed documentation by the individual civilizations (Reed, 1977).

This long history of agriculture enabled farmers to pick up environmental ‘hints’ that led to a rich harvest of crops.  Among the various abiotic and biological indicators that were available to them, the presence of particular plant species or a community of plant species was an indicator commonly used to assess soil quality.  Use of such ‘indicator plants’ on a particular piece of land to determine suitable crop plants to be cultivated is documented as early as 50 AD by Pliny the Elder (23-79 AD, author of Naturalis Historia; Sampson, 1939).  Unfortunately, documentation of such studies or knowledge were rare until the early 1900s (Clements, 1920; Hursh and Crafton, 1935).  An extensive early review on plant indicators was compiled by Sampson (1939).  The following key points concerning soil quality indicators in particular were raised:

  • a community of plant species is a better indicator than just a single species to assess soil condition
  • ‘characteristic species’ that are ecologically specialized to a particular environment serve as good indicators (in comparison to more common species)
  • the reliability of plant species as indicators is highly dependent on the knowledge of the ecological relations between the native vegetation, suitable crop of interest and environmental variables (and therefore thorough research on the relationship of these factors is critical for the vegetative observations to have value)
  • native perennial vegetation, in particular tree species are better indicators than annual species
  • annual species are good indicators of grazing pressure
  • deficiency of particular nutrients can be detected by change in colour of leaves in certain plant species (e.g. nitrogen deficiency can be detected by leaf discolouration in hemp and buckwheat)

In a more recent review on the use of weed species community structure to assess soil condition, Hill and Ramsay (1977) compiled a list of weed species and under what condition it was found to grow.  This review raises a point that the weed species/soil condition relationship is not a definite one, and that the list should be used as an opinion, rather than an answer to a particular problem.

Current studies on indicators of soil quality are focusing on community structures of microorganisms such as bacteria and fungi (Chen et al., 2003; Winding et al., 2005; Toljander et al., 2006).  One patent application that utilizes the concept of screening community structure to assess soil condition uses single nucleotide polymorphisms to investigate nematode diversity (WO 2004/090164).  These studies on microbial community structure lead to isolation of certain microorganisms that can further be genetically engineered to become powerful tools as sensitive bioindicators that detect specific substances in the environment.

Current methods to measure soil condition

Current available methods to measure soil parameters involve a colorimetric system.  The sample is combined with a substrate that causes a chemical reaction between a nutrient of interest within the sample (e.g. nitrogen, phosphate, potassium) and the substrate that produces colour, the intensity of which is then measured using photometers.  Laboratories conduct tests for farmers, however problems such as sampling cost and effort, and delays in obtaining results has deterred farmers from utilizing such services.  As an alternative to sending samples to laboratories, there are relatively inexpensive, field-based test kits available in the market.  Many portable test kits are supplied by various companies includingPalintestAquaticLife, Rapitest, LamotteMilwaukee InstrumentsHachELE, and Merck.  Limitations with these portable test kits are inconsistancy in results due to sampling and testing variation or error (Daniels et al., 2001), accuracy (laboratory results will provide more accurate results), and complexity of use with certain kits (and therefore necessity for training).

In all cases, they do not provide the opportunity to continuously monitor the environment – in other words, early detection of conditional deterioration is difficult with the colourimetric system unless routine monitoring can be conducted.

Proposals of alternative methods to assess environmental conditions – Transgenic biosensors that respond to particular conditions

A number of scientists in educational institutions have expressed optimism about the use of genetic engineering to produce transgenic bioindicator organisms that can detect nutrient deficiency in a particular environment (Ollinger et al., 2003; Sobral, 1997; Sandhana, 2003; MJ Hawkesford lab website,; CEBIOVEM,  Research in the field of nutrient deficiency detection has been concentrating on identifying genes that are upregulated during starvation of particular nutrients, isolating the promoter region of such genes, and linking them with reporter genes.  Examples of such systems and transformed organisms include PSQD1::GUSinto A. thaliana (P deficiency; Hammond et al., 2003), PphoA::luxCDABE into P. fluorescens and E. coli (P deficiency; Dollard and Billard, 2003), PphoA::luxAB into a Synechococcus sp. (P deficiency; Schreiter et al., 2001), PglnA::luxAB into a Synechococcus sp. (N deficency; Gillor et al., 2003), PnarG::inaZ and PnarG::GFP into E. cloacae (N deficiency; DeAngelis et al., 2005), and PisiAB::luxAB into a Synechococcus sp. (Fe deficiency; Durham et al., 2002).  However, the technology of this field is still in early stages of research and development.

One patent family (WO 1994/13831: A highly sensitive method for detecting environmental insults by E.I. du Pont de Nemours and Co.; see chapter 5 – Detection of metal and other toxic compounds) contains granted patents in Canada (CA 2150232), Europe (EP 673439) and the United States (US 5683868), which generally claims a method to detect change in environmental conditions using a bioindicator organism.  This patent family provides examples of transgenic E. coli strains that can detect nitrogen and phosphate limitation.

A team lead by Dr Anthony Trewavas at the School of Biological Sciences, Edinburgh University was reported to have developed a transgenic potato that can detect dehydration in 1999 (, but we were not able to identify a scientific article or any patent documents  concerning this research.



Blake-Kalff MMA, Zhao FJ, Hawkesford MJ, McGrath SP (2001). Using plant analysis to predict yield losses caused by sulphur deficiency. Ann. Appl. Biol. 138:123-127.

Clements FE (1920). Plant indicators: the relation of plant communities to process and practice. Carnegie Inst. Wash., Publ. No. 290. 388 pp.

Daniels MB, Delaune P, Moore PA Jr, Mauromoustakos A, Chapman SL, Langston JM. (2001). Soil phosphorus variability in pastures: implications for sampling and environmental management strategies. J Environ Qual. 30(6):2157-65.

DeAngelis KM, Ji P, Firestone MK, Lindow SE (2005). Two Novel Bacterial Biosensors for Detection of Nitrate Availability in the Rhizosphere. Appl Environ Microbiol 71(12):8537–8547.

Hill SB, Ramsey J (1977). Weeds as Indicators Of Soil Conditions. Faculty of Agricultural and Environmental Sciences, McGill University, Quebec, Canada.

Hursh CR, Crafton WM (1933). Plant indicators of soil conditions on recently abandoned fields. US Department of Agriculture, Forest Service, Appalachian Forest Experiment Station,

Ollinger S, Sala O, Ågren GI, Berg B, Davidson E, Field CB, Lerdau MT, Neff J, Scholes M, Sterner R. (2003). New Frontiers in the Study of Element Interactions.

Reed CA ed. (1977). The Origins of Agriculture. Mouton, The Hague.

Sampson AW (1939). Plant indicators– concept and status. Bot. Rev. 5: 155-206.

Sandhana L (2003). Plants: New Anti-Terror Weapon?,1282,58118,00.html (news article on Dr Jack Schultz and funding from the Defense Advanced Research Projects Agency to develop transgenic A. thaliana that can detect explosives)

Sobral BWS (1997).  Genetic tools for a sustainable future.

Toljander JF, Eberhardt U, Toljander YK, Paul LR, Taylor AF. (2006).  Species composition of an ectomycorrhizal fungal community along a local nutrient gradient in a boreal forest. New Phytol. 170(4):873-84.

Vasey DE (1992).  An Ecological History of Agriculture: 10,000 B.C. – A.D. 10,000.  Iowa State University Press.

Winding A, Hund-Rinke K, Rutgers M (2005).  The use of microorganisms in ecological soil classification and assessment concepts.  Ecotoxicol Environ Saf. 62(2):230-48.


Dollard MA, Billard P. (2003).  Whole-cell bacterial sensors for the monitoring of phosphate bioavailability.  J Microbiol Methods 55(1):221-9

Gillor O, Hadas O, Post AF,  Belkin S. (2002).  Phosphorus bioavailability monitoring by a bioluminescent cyanobacterial sensor strain.  J Phycol. 38:107-115.

Hammond JP, Bennett MJ, Bowen HC, Martin R. Broadley MR, Eastwood DC, May ST, Rahn C, Swarup R, Woolaway KE, and White PJ (2003).  Changes in gene expression in Arabidopsisshoots during phosphate starvation and the potential for developing smart plants.  Plant Physiol. 132:578-596.

Schreiter PP, Gillor O, Post A, Belkin S, Schmid RD, Bachmann TT. (2001).  Monitoring of phosphorus bioavailability in water by an immobilized luminescent cyanobacterial reporter strain.  Biosens Bioelectron. 16(9-12):811-8.


Chen G, Zhu H, Zhang Y (2003).  Soil microbial activities and carbon and nitrogen fixation.  Res Microbiol.154(6):393-8.

Gillor O, Harush A, Hadas O, Post AF, Belkin S (2003).  A Synechococcus PglnA::luxAB fusion for estimation of nitrogen bioavailability to freshwater cyanobacteria.  Appl. Environ. Microbiol. 69:1465-1474.


Durham KA, Porta D, Twiss MR, McKay RML, Bullerjahn GS (2002).  Construction and initial characterization of a luminescent Synechococcus sp. PCC7942 Fe-dependent bioreporter. FEMS Microbiol Lett. 209:215-221.