Many bacterial species from diverse phyla have the ability to fix nitrogen, including many (but not all!) cyanobacteria, actinobacteria and proteobacteria. The nitrogen fixation genes are thought to have spread between distantly related bacteria by horizontal gene transfer of clusters of nitrogen-fixation (nif) genes. Nitrogen-fixing bacteria, also called ‘diazotrophs’, can be free-living in water or on solid substrates like soil or rocks. More than half of the biological nitrogen fixation on earth stems from nitrogen-fixing marine bacteria, the rest from terrestrial sources (Fowler et al. 2013). Terrestrial N₂-fixing bacteria are found in the soil, in aquatic, and often extreme, habitats, such as hot springs, and nutrient-poor areas. Much of the action of N₂-fixing bacteria happens in soils. Plants can then use nitrogen released by decay of such organisms.

However, some plants have evolved a tighter relationship with N₂-fixing bacteria, involving an exchange of carbon and nitrogen between plant host and bacterial partner (Santi et al. 2013). Several different symbioses of this type have evolved independently (Table 4.2), from primitive algae to higher vascular plants. These associations are characterised by active attraction of the symbiotic partner through metabolites or signals from the host, as well as a physical housing of the symbiont inside the host (Delaux et al. 2015). For example, algae can form a symbiosis with N₂-fixing cyanobacteria to form lichens, and Bryophytes like Anthoceros harbor N₂-fixing cyanobacteria in cavities of their thalli. Roots or leaves of some plants form a loose association with N₂-fixing bacteria, with plant exudates used as a carbon source by the bacteria. In the water fern Azolla, the cyanobacterium Anabaena is located in cavities on the underside of modified leaves, with a secretory trichome delivering sugars and absorbing fixed nitrogen. This symbiosis is especially important in rice paddy fields, where Azolla densely covers the water surface and can then be incorporated into the field soil. In other plants, the N₂ fixers are located in intercellular spaces of the host plant, as reported for sugarcane. These less intimate associations supply host plants with substantial amounts of nitrogen. While such associations have been explored for other grasses, the likely limitation for substantial nitrogen fixation in these loose associations is the limited amount of carbon that the plant provides for its symbionts.

In more highly developed associations, plants localise the symbiotic association within a modified root or ‘nodule’. In cycads, the microsymbiont Anabaena is located in intercellular spaces of the mid-cortex of short, highly branched, modified roots (Figure 4.40a and b). In another class of symbioses, the actinorhizal plants, the micro-symbiont Frankia (an actinomycete, or filamentous bacterium) is located within the cortical cells of a modified root. This group includes the genera Casuarina, Allocasuarina, Alnus, Datisca and Myrica from eight plant families, all belonging to the Rosid I class, as do legumes (Figure 4.40c and d). These plants often grow in nutrient-poor habitats where nitrogen fixation provides a nutritional advantage. Parasponia, a tropical tree native in New Guinea, is the only non-legume known to form a symbiosis with the rod-shaped bacterium Rhizobium. Unlike legumes, the Parasponia nodule has a central vascular bundle and the microsymbiont is always encapsulated within cellulosic material (termed a ‘persistent infection thread’). In legumes, nodules typically have a central infected zone, and rhizobia are enveloped by plasma membrane-derived vesicles called symbiosomes (Figure 4.40e and f).