Why we DO NOT Recommend the use of Beneficial Mycorrhizae (Fungi) and Bacteria in Hydroponics!
Mycorrhizae are beneficial fungi that penetrate the roots of most plants in nature. This symbiotic relationship is beneficial in that the plant provides sugars to the fungi, and the fungi enhance nutrient uptake for the plant. There are two major groups of mycorrhizae: ectomycorrhyzae and endomychorrhizae. The 'ectos' do not actually penetrate the cells of the roots, but are found between the intercellular spaces. Ectos have been found to be able to utilize a range of organic compounds such as proteins, peptides and amino acids (1, 5, 7,). However, these fungi are restricted to coniferous tree species (gymnosperms) and Ericacious (heath/ bog) species where soil breakdown of amino acids is minimal (1, 2, 5).  

Endomycorrhizal fungi aid in water and nutrient uptake, especially phosphorus, but do not aid in mineralization of organic matter, and thus have not been found to take up organic nutrients (1-7). Unlike ectos, 'endos' invade root cortical cell walls and can form branched structures called arbuscules which are efficient sites of exchange between fungus and root cell. Endos are primarily associated with herbaceous plants (angiosperms) commonly grown in greenhouses and hydroponic systems (1-7).

In hydroponics, there would be little value to be obtained from mycorrhizal associations in this situation. Their value is to provide improved uptake of water and minerals from the soil / growing media. In a hydroponic setting, the plant has constant access to all the water and dissolved minerals it needs. The mycorrhizal fungi would do little to improve on a root constantly bathed in water and minerals, however may aid in nutrient uptake under plant stress and low root biomass (3, 8). Most hydroponically grown plants are of angiosperm origin, and since endomycorrhizae are not known to take up whole organic molecules in any situation, these fungi would not benefit in the uptake of a root based supplement product containing these substances. Many products make claims of enhanced growth and yield from beneficial microorganisms added to the nutrient solution along with organic fertilizers. This phenomenon can be attributed to the enzymatic secretions of these fungi into the solution to breakdown organic matter into its essential elements for uptake and transport to the roots (8, 9). Essentially, it is the same as adding extra fertilizer.

In soil mediums where organic fertilizers are used, the extra surface area provided by the mycorrhizal associations can act to enhance nutrient uptake, and to break down (via enzymatic secretions from the fungi) organic matter into its essential minerals useable by plants. Beneficial bacteria are useful in this situation again by breaking down organic matter and rendering it useful to plants in its simple mineral form. Organic fertilizers are slow acting and slow releasing, and these beneficial organisms are necessary in situations where no added mineral salts are present. However, there is little to be gained even in soil and soilless mediums when complete fertilizers with all essential nutrients are present. The use of  Beneficial Bacteria in hydroponic systems can clog lines, filters and pumps.