There is still debate in the scientific community as to why plants form phytoliths, and whether silica should be considered an essential nutrient for plants. Studies that have grown plants in silica-free environments have typically found that plants lacking silica in the environment do not grow well. For example, the stems of certain plants will collapse when grown in soil lacking silica. In many cases, phytoliths appear to lend structure and support to the plant, much like the spicules in sponges and leather corals. Phytoliths may also provide plants with protection. These rigid silica structures help to make plants more difficult to consume and digest, lending the plant's tissues a grainy or prickly texture. Phytoliths also appear to provide physiologic benefits. Experimental studies have shown that the silicon dioxide in phytoliths may help to alleviate the damaging effects of toxic heavy metals, such as aluminum. Finally, calcium oxalates serve as a reserve of carbon dioxide. Cacti use these as a reserve for photosynthesis during the day when they close their pores to avoid water loss; baobabs use this property to make their trunks more flame-resistant.
According to Dolores Piperno, an expert in the field of phytolith analysis, there have been four important stages of phytolith research throughout history.
First, soluble silica, also called monosilicic acid, is taken up from the soil when plant roots absorb groundwater. From there, it is carried to other plant organs by the xylem. By an unknown mechanism, which appears to be linked to genetics and metabolism, some of the silica is then laid down in the plant as silicon dioxide. This biological mechanism does not appear to be limited to specific plant structures, as some plants have been found with silica in their reproductive and sub-surface organs.
Phytoliths are composed mainly of noncrystalline silicon dioxide, and about 4% to 9% of their mass is water. Carbon, nitrogen, and other major nutrient elements comprise less than 5%, and commonly less than 1%, of phytolith material by mass. These elements are present in the living cells in which the silica concretions form, so traces are retained in the phytoliths. Such immobilised elements, in particular carbon, are valuable in that they permit radiometric dating in reconstructing past vegetation patterns. The silica in phytoliths has a refractive index ranging from 1.41 to 1.47, and a specific gravity from 1.5 to 2.3. Phytoliths may be colorless, light brown, or opaque; most are transparent. Phytoliths exist in various three-dimensional shapes, some of which are specific to plant families, genera or species.
Phytoliths may form within single cells, or multiple cells within a plant to form 'conjoined' or multi-cell phytoliths, which are three-dimensional replicas of sections of plant tissue. Conjoined phytoliths occur when conditions are particularly favourable for phytolith formation, such as on a silica rich substrate with high water availability