Root Microbiome and its Ecological Functions

Srabani Roy Chowdhury, MAKAUT, WB

Introduction

Plant roots are associated with a diverse community of microorganisms. These communities are collectively known as root microbiome. The communities contain microorganisms that are both helpful as well as harmful for the plant, in terms of affecting its physiological functioning. Mycorrhizal and mycoparasitic fungi as well as bacteria that fix nitrogen alongside promoting plant growth are some helpful microorganisms of this community. The root microbiome is responsible for numerous host plant mechanisms and fitness. They not only benefit themselves from their host but also take part in host body mechanisms. The nature of interaction might differ from one host to another.

Constituents of the Root Microbiome

There have been numerous reports on various rhizosphere organisms over the years. Some show beneficial effects on plant growth. These are the nitrogen-fixing bacteria, mycorrhizal fungi, biocontrol microorganisms, mycoparasitic fungi, and protozoa. Rhizosphere organisms that are not beneficial to plant growth include pathogenic fungi, oomycetes, certain bacteria, and nematodes. Human-derived pathogens also occur in the rhizosphere.

Bacteria

Plant root contains a unique nutritional environment that mixes into the surrounding soil. This promotes the growth of both beneficial and harmful bacteria. Amongst these bacteria, a beneficial bacterial community helps by preventing the attack of pathogenic microbes. They mostly attach to the surface by chemical action (chemotaxis), or with the help of flagella-like structures. A few can also reach the inner root of the host plants, after colonization. Rhizobacteria is the most common type of bacteria associated with leguminous roots. They help by-

• Production of Nod signaling factors to induce nodule formation. They help in the nitrogen fixation of the plants by converting gaseous Nitrogen into ammonia. The host provides the bacteria with amino acids and is exchanged for nitrogen-fixed amino acids. This enhances plant growth.
• The symbiotic relationship between the rhizobacteria and host plants is very remarkable as well. The bacteria provide the host with essential nutrients and the host in exchange provides it necessary conditions for the bacteria to survive.
• Promotes plant growth after colonising its roots.

Azospirillum is a bacterial species that produces phytohormones that help in the growth of the root hairs. As the root hairs grow, they start occupying a larger surface area and help in accumulating more nutrition for the plant. Therefore, it also helps in overall plant growth.

Archaea

Archaeal communities are generally found in extreme environmental conditions. But due to their ubiquitous nature, they are found almost everywhere including the root microbiome. For example, root colonizing Archaea are abundantly found in mangroves. Also found in rice, maize, and wheat. The presence of Archaea in soil determines the presence of an important group of ammonia oxidizers. The Archaea found in the roots of plants belonging to anaerobic soil or wetlands are ammonium and methanogen oxidizing archaea. Due to its nature of tolerating extreme conditions, they provide tolerance against stress, insects. They also enhance nutrient uptake and growth of the plants.

Fungi

Broadly classifying there are two types of fungi found in the root microbiome. They are

• Mycorrhizae- Most important plant-fungi interaction. It plays a vital role in the plant-soil relationship as well as the relationship with other plants. They are present in the roots of all plants.
• Endophytes- They grow and colonize inside the intracellular spaces of the root tissues. Though they provide tolerance against many stressful conditions, they are mostly pathogenic.

Viruses

Virus communities are also found in the root microbiome. They are mostly pathogenic and cannot enter the root tissues without a vector. Zoosporic fungi or nematodes are the common vectors.

Assembly Mechanism

Assembly mechanism refers to the classification of individual root microbes into different communities. The taxonomy of microorganisms within root microbial communities depends on the surrounding soil. Due to various unique niches present in the rhizosphere, the relative abundance of various taxonomy might differ widely. An ecological niche refers to the match that is found in different species for a specific environmental condition. According to ecological niche, the assembly mechanisms for root microbiome are-

Biotic Assembly Mechanism

The various microbial communities present in the root microbiome are associated with different parts of a root. For example, the main root along with its branches of fine roots and root tips are associated with a particular set of microbial communities whereas the rhizosphere, root surface, and tissues deal with different communities. This happens mainly due to the different chemical compositions of these regions. Microbial communities also differ from one plant species to another because the host-specific immune response and presence of different carbon root exudates vary from one plant to another. Root microbial community composition is also affected by how old the host plant is. Neighboring vegetation also plays an important role in shaping the composition of the microbial community of a plant’s root.

Abiotic Assembly Mechanism

Various abiotic mechanisms also shape the composition of the root microbial community. This is because different factors can affect the biotic assembly. For example, different temperatures, pH, moisture, a nutrient present in the soil, and other climatic factors can affect the biotic assembly mechanism of root microbial communities.

Ecological Functions

Microbial communities present in the roots play a vital role in plant mechanisms. Three types of microorganisms are found in the rhizosphere- one that is beneficial for the plant, second that is pathogenic and attacks the immune system and causes diseases. The third type of microorganisms is human pathogenic microbes that contain in the root tissues and can cause serious threats to humans. Rhizosphere microorganisms are known as bio-indicators of soil quality. This is because they are highly sensitive to minute changes in abiotic conditions. For example, perturbation, environmental stress, etc.

The Good Microbiome:

• Improves host immunity- The root microbiome is highly responsible for modulating the plant immune system. For example, Rhizobacteria contains quorum-sensing molecules that help in the activation of defense-related genes like MPK3, MPK6, etc.
• Increases nutrition uptake- The nutrient status of a plant is highly influenced by the members of the root microbial community. For example, nitrogen fixation by rhizobia and phosphorous uptake by mycorrhizal fungi.
• Improves plant metabolism.
• Provides resistance against pathogenic microorganisms and environmental stress- The microbial community present in the roots provides a defense against various soilborne pathogens. They are capable of antagonizing the pathogens during primary infection itself. They also help plants survive and support their growth in extreme environmental conditions. 
• Induces bio fertilization and rhizoremediation.
• Stimulates growth of roots.

The Bad Microbiome

• Reduces plant performance by competing for limited nutrients.
• Induces different plant diseases.
• Attacks the plants as pathogens.
• Alters the ecological functions associated with the host.
• Reduces yield and causes economic damage.

Conclusion

The root microbiome has shown positive signs in plant body functions, but those functions are yet to be explored. It is believed that deciphering these functions will lead to crop improvement and protection of crops from various microbial communities. Different microbial communities have been found to support plant growth under biotic and abiotic stress. However, the pathogenic part of the root microbiome is a reason for concern. Plant pathogens can cause economic damage due to a reduction in yield. Human pathogenic microbe contamination of the food chain is also considered to be a serious issue. We should develop different strategies to keep plant and human pathogens under control. These strategies will help the rhizosphere microbial community to redirect towards microorganisms that prevent pathogens from growing, attaching, and invading the root tissue.

Also read: Allosteric signaling with co-evolutionary history

References:

• Fitzpatrick, C. R., Copeland, J., Wang, P. W., Guttman, D. S., Kotanen, P. M., & Johnson, M. T. J. (2018). Assembly and ecological function of the root microbiome across angiosperm plant species. Proceedings of the National Academy of Sciences, 115(6), E1157–E1165. https://www.pnas.org/content/115/6/E1157

• Garcia, K., Bücking, H., & Zimmermann, S. D. (2020). Importance of Root Symbiomes for Plant Nutrition: New Insights, Perspectives and Future Challenges. Frontiers in Plant Science, 11, 594. https://doi.org/10.3389/fpls.2020.00594

• Mendes, R., Garbeva, P., & Raaijmakers, J. M. (2013). The rhizosphere microbiome: Significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiology Reviews, 37(5), 634–663. https://doi.org/10.1111/1574-6976.12028

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