Microbial-Plant Associations

	Various associations exist between microbes and plants in both the phyllosphere and the rhizosphere. Associating in the phyllosphere is more difficult generally, as it requires protection from UV radiation, fast temperature changes, and high dessication. Hence phyllosphere associations are more inconsistent. In the rhizosphere, temperature changes gradually and there is significantly less dessication; UV is no longer an issue. Hence a much greater number of associations exist between microbes and plant roots.
	Microbes function to cycle elements and nutrients in and around the root system, as well as produce organic acids which solubilize materials like apatite and leave behind things like phosphate. Microbes may also produce gibberellins or auxin which cause growth of the roots. Potential pathogens can also be inhibited by production of antibiotics or bacteriocidal peptides.
	A very successful association exists between fungus and roughly 80% of vascular plants; mycorrhizae. In this association, fungus integrates into the root either as an endo- or ecto-symbiont.
	In ectomycorrhizae, fungal hypha intertwine around the root and prevent pathogen attachment, but also restrict root hair formation. However the root is able to utilize the fungus in the place of root hairs, which gives a much greater surface area. The plant ends up giving about 60-80% of photosynthetic products to the fungus in this situation, which is the fungi’s sole source of carbon.
	In endomycorrhizae, fungi have penetrated into the root cells. They exist as arbuscular or vesicle forms (VA) or ericoid forms (usually ascomycetes). Fungus actively  absorbs elements from soils, while the plant provides carbon. Endosymbiotic bacteria like Burkeholdena in the fungi may also function in nutrient cycling or nitrogen fixation. The action of the fungus absorbing nutrients increases the nutrition the plant obtains from the soil.
	Another association exists with Rhizobium which forms root nodules allowing for nitrogen fixation. A specific Rhizobium interacts with a specific legume after being attracted by exudates. Division occurs and a potential quorom sensing mechanism leads to production of bacteriocins and lipooligosaccharides which are dictated by the Nod genes. Specificity is determined by length and modifications of the LOS’, and is adhesion is aided by rhicadhesin which binds to calcium complexes on the root hair surface at the tip. Tryptophan from the root is metabolized to indoleacetic acid which forms an envagination in the root hair, which develops into an infection thread for transport of Rhizobium inwards. At some point, Rhizobium is triggered to differentiate almost all of its population by swelling, branching, degrading their chromosomes and expressing nitrogen fixation genes from the nif/nix operons. The plant produces leghemoglobin in order to supply the now bacteroid with oxygen for ATP production and small organics as electron sources. This ATP is used to fix nitrogen, some of which is incorporated into amino acids, but most of which is secreted as glutamine.
	Another important association exists between Anabaena azollae and Azolla, a water fern. The Azolla fronds contain small pores in which Anabaena colonizes and fixes nitrogen in flooded rice paddies. Rice is then planted between the Azolla and outcompetes it, leading to the release of nitrogen into the flooded paddy and growth of SRB’s which produce sulfide. Beggiatoa then colonizes the root surface of the rice plants and oxidizes sulfide which the rice utilizes, while taking oxygen from the rice plant.
	Agrobacterium tumafaciens associates with plants in a pathogenic way by causing the formation of crown galls on wounds near the base of the plant. Agrobacterium is attracted to phenols produced after wounding, and attach via fimbrium and a cellulose-like material. A series of virulence genes produce a type IV secretion system and extracts the tDNA from the plasmid and stabilizes it in the cytoplasm. tDNA is transported into the target cell, and it contains two genes, onc (oncogene) and ops (opine synthesis gene). Opines are utilized by the bacteria for metabolism, and the oncogene stimulates uncontrolled growth of the cell. This mechanism can be used as a vector for delivery of plasmids of interest to plant tissues, such as for example herbicides or insecticides.