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The whole mass of living organisms in soil is called its microbial biomass. The microbial biomass can be estimated by measuring the amount of carbon, nitrogen, phosphorus or sulfur that is present in the microorganisms in the soil. There are a number of different ways of measuring microbial biomass.
The number of individual soil animals in the soil is enormous. In all but the driest environments there are billions of protozoa per square metre (m²), millions of nematodes/m² and 100,000’s of mites/m². In a pasture soil from east Beverley in Western Australia there were approximately 800 million protozoa, 900,000 nematodes and 130,000 mites per square metre.
Soil organisms are identified by studying their:
Rhizobia are one of the groups of microorganisms living in soil. They can form a mutually beneficial association, or symbiosis, with legume plants. Rhizobia are very difficult to identify from their shape or size alone because all forms are extremely small, short rods with rounded ends.
New methods of rhizobia characterisation have been developed using DNA patterns from known rhizobia grown under laboratory conditions. Comparisons are made between sections of the known DNA molecule that code for particular functions (e.g. nitrogen fixation) with samples of DNA from soil or from a root nodule. This tells the scientists whether there are genes for that function in the soil sample or root nodule.
Serological techniques can also be used to identify rhizobia. Samples of known bacteria are injected into an animal under specific laboratory conditions. The animal's body produces antibodies against the bacteria. (A process that is similar to vaccination). The component of the blood containing the antibodies is the serum and this is separated from the red blood cells. This is called antiserum.
The antiserum produced by the animal can be collected and used to help locate bacteria in a sample. The antibodies in the antiserum can be joined to a fluorescent dye or to an enzyme with an attached dye. When the antibody is added to the corresponding bacteria it attaches firmly. The bacteria can then be identified using a fluorescence microscope or in a solution that contains a molecule that can interact with the enzyme and cause a colour change in the solution. This method is called the ELISA method.
The antiserum can be chosen to be very specific for particular types of rhizobia, so it is a good way to identify whether those rhizobia are present in a root nodule. It is often important to know whether the rhizobia that were added with the seed have actually been responsible for forming the nodules on the legume or whether other rhizobia already in the soil formed the nodules.
In the 1880's, a scientist named Koch proposed a method for identifying the organism responsible for a disease. When his procedure is applied to identifying plant diseases the following must occur for the identification to be successful:
An organism is isolated from a plant showing symptoms of the disease.
The organism is grown separately from other organisms and the host (on an artificial food source).
The organism is placed into contact with a healthy plant and the plant develops the same symptoms of the disease.
The organism is isolated from the second diseased plant.
Soil nitrogen supply is the release nitrogen crop residues and organic matter in soil as they are decomposed by microorganisms. Soil nitrogen supply is currently measured in the laboratory using a method that takes a week to complete. This method is thus both too costly and slow for use as a decision support tool for fertiliser application rates.
However, in the future it may be possible to use mid infrared technology to measure soil nitrogen supply quickly and inexpensively. The advantage of the mid infrared technology is that once it is established, soil samples can be collected from the field and scanned in approximately 2 minutes per sample. This considerably decreases analytical costs meaning that growers could afford to have more soil samples analysed enabling spatial maps to be generated or deeper soil layers to be assessed.
Mid infrared is not as accurate as measuring soil nitrogen supply by standard analytical techniques. However, it may be useful for developing maps of soil nitrogen supply across a farm. These maps could be used to allow for variable application rates of nitrogen fertiliser to be applied.
For example, soil was collected under an oat crop at Dangin in 2003 using a 25m x 25m sampling grid (180 separate sampling points over 10 hecatres). Soil nitrogen supply was measured using standard laboratory methods and also predicted using mid infrared technology. This intensive sampling grid was used for assessing the required sampling grid size for farm management application. The spatial maps below show that there was good agreement between soil nitrogen supply as measured using the standard technique (Figure 1) and as predicted using mid infrared (Figure 2).
This data suggests optimal crop yields would require additional fertiliser to be applied to the red and yellow areas. In a good rainfall year, low fertiliser nitrogen application would also be of benefit in the light blue area. Fertiliser nitrogen may not be economic on the dark blue areas as soil nitrogen supply is already sufficient to satisfy the crop’s demand for nitrogen.
Figure 1. Standard laboratory detection of biological soil N supply – Data from soil samples (0-10 cm) collected on a 25 m x 25 m sampling grid. Colours areas where biological soil N supply was categorised into 4 ranges: red = very low, yellow = low, light blue = moderate and dark blue = high (data courtesy of Daniel Murphy and Nui Milton, the University of Western Australia).
Figure 2. Mid infrared predicted biological soil N supply – Data for the same 10 ha area as that shown in Figure 1 (i.e. the pattern of colour on figure 2 would be identical to that on figure 1 if the mid infrared prediction was 100% accurate). The same colour groupings apply (data courtesy of Daniel Murphy and Nui Milton, the University of Western Australia).