When a biological system is in existence in your soil profile, the need to fertilise with biological products still exist, but your input costs are much lower due to the fact that the symbiotic relationship with the plant roots and the soil biology is working to build the soil food web. You may ask: How does this happen?
The plant’s fine root hairs exude liquid exudates into the plant’s rhizosphere (the region of soil around the roots in which the plant’s chemistry and microbiology are influenced through growth, respiration, and nutrient exchange). Plant exudates are used by soil bacteria, fungi, plus many other soil micro-organisms as a food source. While feeding on these exudates, the soil micro-organisms excrete carbon. In exchanging exudates from the root hairs, the plant receives the minerals it requires from the soil to utilise in plant growth or reproduction by way of fruiting or flowering.
For example, if a plant requires copper, the soil biology in association with help from mycorrhizal fungi supplies the copper from the soil profile to the plant root hairs. The mycorrhizal fungus is a network of fine white hairs spread throughout the soil profile which can spread many metres away from the plant, and supply the required copper in our example. This natural way of growing strengthens the plant’s immune system against insect or pathogenic fungal attacks by increasing the plant’s natural sugars. Not only do the plant’s higher natural sugars act as a defence mechanism, but as an added benefit, they increase the flavour of fruits, nuts, berries and vegetables, as well as the intensity of colours in cut flowers, and they enhance the length of the flowering period of plants which in turn increases crop yield.
In his book, “Teaming With Fungi”, Jeff Lowenfels writes that…” A staggering 80 to 95 per cent of all terrestrial plants form symbiotic relationships with mycorrhizal fungi”. IF you use synthetic fertiliser, then this symbiotic relationship is impaired or does not exist.
When plants are force-fed synthetic nutrients in a salt form, then the soil just becomes a medium to hold the plant up. Because the plant’s natural system is not being used, then the plant and the whole crop are set up for insect and pathogenic fungal attack, and guess what, ironically, the same company that supplied you the synthetic fertiliser just so happens to be able to supply sprays to control insects or pathogenic fungal attack.
To understand whether your crop needs to be dominated by bacteria or fungi, there is an easy guide. If your crop is in the ground LONGER than 12 months, then the soil profile needs to be dominated by beneficial fungi. However, if your crop is mostly in the ground LESS THAN 12 months, then the soil profile needs to be bacterially dominated, and with pasture/grass a 50/50 split between beneficial fungi and bacteria is required.
Diagram of the below shows the ground interactions of a nodulated legume with a variety of microbes. A,Enlarged view of nitrogen-fixing nodules on the plant’s roots (circled). B, Ectomycorrhizal associations are often established with legume tree roots, but the fungi remain external. C, Arbuscular mycorrhizal fungi interact with legume roots utilising the same symbiotic pathway as used by Rhizobium. D, Gram-negative bacteria in the soil, such as Pseudomonas, Klebsiella, and Ochrobactrum spp. are established in the rhizosphere and some species may even nodulate legumes. E, Gram-positive microbes, including Bacillus, Paenibacillus, Lysinobacillus, and others are found in the rhizosphere and also within nodules. F,Actinomycetes, for example, Micromonospora, Streptomyces, and the nitrogen-fixing Frankia enhance plant growth.
For decades, rhizobia were thought to be the only nitrogen-fixing inhabitants of legume nodules, and biases in culture techniques prolonged this belief. However, other bacteria, which are not typical rhizobia, are often detected within nodules obtained from soil, thus revealing the existence of a phytomicrobiome where the interaction among the individuals is not only complex, but also likely to affect the behavior and fitness of the host plant. Many of these nonrhizobial bacteria are nitrogen fixers, and some also induce nitrogen-fixing nodules on legume roots. Even more striking is the incredibly diverse population of bacteria residing within nodules that elicit neither nodulation nor nitrogen fixation. Yet, this community exists within the nodule, albeit clearly out-numbered by nitrogen-fixing rhizobia. Few studies of the function of these nodule-associated bacteria in nodules have been performed, and to date, it is not known whether their presence in nodules is biologically important or not. Do they confer any benefits to the Rhizobium-legume nitrogen-fixing symbiosis, or are they parasites/saprophytes, contaminants, or commensals? In this review, we highlight the lesser-known bacteria that dwell within nitrogen-fixing nodules and discuss their possible role in this enclosed community as well as any likely benefits to the host plant or to the rhizobial inhabitants of the nodule. Although many of these nodule inhabitants are not capable of nitrogen fixation, they have the potential to enhance legume survival especially under conditions of environmental stress. This knowledge will be useful in defining strategies to employ these bacteria as bioinoculants by themselves or combined with rhizobia. Such an approach will enhance rhizobial performance or persistence as well as decrease the usage of chemical fertilisers and pesticides.
The fixation of atmospheric nitrogen (N2) into ammonia by bacteria is essential for plant productivity, especially in N-poor soils. About 60% of the fixed N on Earth results from biological nitrogen fixation whereas chemical fertilisers account for ca. 25% (†). The Green Revolution of the last century resulted in crops that produced higher yields. However, the improved crops relied heavily on chemical particularly nitrate fertilisers, which resulted in ground water pollution and negative effects on human health (†). Since the late 20th century, scientific research has focused mainly on plant biotechnology to improve crop productivity, but in this century, scientists are renewing interest in nitrogen-fixing microbes as well as the beneficial bacteria that act as plant growth-promoting rhizobacteria/bacteria (PGPR/PGPB). We propose that the rhizobia and the “other” bacteria act together as a community within the root nodule to facilitate plant health and survival, particularly under conditions of environmental stress.
The phytomicrobiome or plant microbiome is defined as all the microorganisms that colonise everything connected to the plant body, i.e., the rhizosphere and the phyllosphere, and includes all the directly associated endophytes and epiphytes (†). Thus, the phytomicrobiome is a subset of the phytobiome, which has been described as plants, their environment, and the organisms that interact with them, and which together influence plant health and productivity (†). Taking a phytomicrobiome-focused perspective concerning the nodule and looking beyond the interaction of a legume with a single nitrogen-fixing species may help us better understand how to grow, fertilise, and protect crops in a sustainable way.
The nitrogen-fixing bacteria that comprise the majority of the microbial population of legume nodules, both α-rhizobia (members of the Alphaproteobacteria, e.g., Rhizobiumand Bradyrhizobium) and β-rhizobia (Betaproteobacteria, e.g., Cupriavidus and Burkholderia (reviewed by †), are the best known and the most studied inhabitants of legume nodules. Even though α- and β-rhizobia are evolutionary divergent, their symbiotic (nod and nif) genes are highly similar suggesting lateral transfer (†; †; †; †). However, legume root nodules contain many other microbial residents. Figure 1 illustrates that in addition to rhizobia (Fig. 1A), a mélange of soil microbes associate with roots (Fig. 1B to F), and many of them (Fig. 1C to F) inhabit the interior of nodules. With regard to fungi, the community in the legume nodule was found to differ greatly from that found elsewhere in the plant and also from nonlegume plants, supporting the idea of a selected and curated microbiome in the nodule (†). Another study showed that inoculating plants with AM fungi changed the bacterial community and improved plant growth most likely because of improved shoot N, P, and K levels (†). Nevertheless, the most commonly isolated members of the legume nodule community outside of rhizobia consist of Gram-positive and Gram-negative bacteria, some of which have the capacity to fix N2 (†; †; †).