Rhizosphere microflora

The rhizosphere, is a hot spot for numerous organisms and is considered as one of the most complex ecosystems on Earth. Microorganisms found in the soil include bacteria, fungi, nematodes, protozoa, algae, viruses etc.

Rhizosphere organisms that have been well studied for their beneficial effects on plant growth and health are; the nitrogen-fixing bacteria, mycorrhizal fungi, plant growth-promoting rhizobacteria (PGPR), biocontrol microorganisms, myco parasitic fungi, and protozoa. Rhizosphere microorganisms that are deleterious to plant growth and health include the pathogenic fungi, bacteria, and nematodes. A third group of microorganisms that can be found in the rhizosphere are the human pathogens.

Plant-Microbe interactions in the rhizosphere

Microorganisms present in the rhizosphere play important roles in ecological fitness of their plant host.

Important microbial processes that are expected to occur in the rhizosphere include;

✓ pathogenesis

✓ plant protection/growth promotion

✓ production of antibiotics

✓ geochemical cycling of minerals

✓ plant colonization

Plant-microbe interactions may thus be considered beneficial, neutral, or harmful to the plant, depending on the specific microorganisms and plants involved and on the prevailing environmental conditions.

Pathogenic interactions

Roots exudates can attract beneficial organisms, but they can also be equally attractive to pathogenic populations. Many pathogenic organisms, bacteria as well as fungi, have coevolved with plants and show a high degree of host specificity. But even though plants are in permanent contact with potential pathogens such as fungi, bacteria or viruses, successful infection is rarely established. Such a general resistance against most pathogens has been named “horizontal resistance”. These resistance mechanisms include structural barriers and toxic compounds that are present in the unaffected, healthy plant. Phytoanticipins; is a toxin which resist the entry and colonization of pathogenic fungi in plants. In some instances, pathogens can overcome the pre-formed barriers and develop virulent infection processes leading to plant disease.

Beneficial microorganisms and modes of action

Plant-beneficial microbial interactions can be roughly divided into three categories. 

First, those microorganisms that, in association with plants, are responsible for its nutrition (i.e., microorganisms that can increase the supply of mineral nutrients to the plant). In this case, most organisms may not directly interact with the plant, but their effects on soil biotic and abiotic parameters  have an impact on plant growth. e.g. Microbes involved in biogeochemical cycles. 

Second, there is a group of microorganisms that stimulate plant growth indirectly by preventing the growth or activity of pathogens. Such microorganisms are referred to as biocontrol agents, and they have been well documented.

 A third group involves those microorganisms responsible for direct growth promotion. For example, by production of phytohormones.

1. Plant growth promoting Rhizobacteria- PGPR  improve plant growth.  PGPR strains have been used successfully for crop inoculations such as Bacillus, Pseudomonas, Rhizobium etc. PGPR  promotes plant growth, development and protection by 

1. Biofertilization -directly, by helping to provide nutrient to the host plant, or helps in root growth and morphology or other beneficial symbiotic relationships- Rhizobium, Azospirillum etc, 
2. Phyto stimulation (plant growth promoting, usually by the production of phytohormones [auxins, cytokinins, and gibberellins) 
3. Biocontrol (controlling diseases, mainly by the production of antibiotics and antifungal metabolites, lytic enzymes etc). Eg., Bacillus thuringiensis (BT)

• Pathogen inhibition can also  be by
• Antagonism, including; Antibiosis i.e. the inhibition of microbial growth by diffusible antibiotics, toxins, and biosurfactants,  
• Competition  for resources such as nutrients and oxygen occur generally in soil between soil-inhabiting organisms. 
• Induced resistance -Plant-associated bacteria can reduce the activity of pathogenic microorganisms by helping the plant to better defend itself, a phenomenon termed “induced systemic resistance”, “ISR”.

Neutral interactions

Saprophytic microorganisms are responsible for decomposition of organic residues in soil and associated soil nutrient mineralization or turnover processes. Whereas these organisms do not appear to benefit or harm the plant directly (hence the term neutral), their presence is vital for soil dynamics, and their absence would influence plant health and productivity.