Revisiting Plant-Microbe Interactions and Microbial Consortia Application for Enhancing Sustainable Agriculture: A Review

Abstract

The present scenario of agricultural sector is dependent hugely on the use of chemical-based fertilizers and pesticides that impact the nutritional quality, health status, and productivity of the crops. Moreover, continuous release of these chemical inputs causes toxic compounds such as metals to accumulate in the soil and move to the plants with prolonged exposure, which ultimately impact the human health. Hence, it becomes necessary to bring out the alternatives to chemical pesticides/fertilizers for improvement of agricultural outputs. The rhizosphere of plant is an important niche with abundant microorganisms residing in it. They possess the properties of plant growth promotion, disease suppression, removal of toxic compounds, and assimilating nutrients to plants. Utilizing such beneficial microbes for crop productivity presents an efficient way to modulate the crop yield and productivity by maintaining healthy status and quality of the plants through bioformulations. To understand these microbial formulation compositions, it becomes essential to understand the processes going on in the rhizosphere as well as their concrete identification for better utilization of the microbial diversity such as plant growth-promoting bacteria and arbuscular mycorrhizal fungi. Hence, with this background, the present review article highlights the plant microbiome aboveground and belowground, importance of microbial inoculants in various plant species, and their subsequent interactive mechanisms for sustainable agriculture.

Keywords: microbial community analysis; microbial inoculants; plant growth promotion; rhizosphere interactions; sustainable agriculture.

FIGURE 1

Associations in the rhizosphere between plant roots, microbes, and root exudates under biotic and abiotic influences.

FIGURE 2

Interactions in the rhizosphere, (A) Plant–microbiome interactions: Plant roots secrete root exudates and phytochemicals that engage microbial populations in developing niches. Some metabolites filter out the unnecessary microbial strains occupied in niches (indicated by red cross), whereas some metabolites allow the different microbial population to coexist in same niche that may secrete compounds needed for growth of other microorganisms. (B) Root–root interactions: The neighboring plants may associate with other forming beneficial, as well as competing interactions by allelochemicals, root exudates, and volatile organic compounds. (C) Microbiome–plant interactions: Beneficial bacteria allow the promotion of plant growth by various mechanisms, such as making nutrients available by chelating them and transporting to plants (for example, siderophore-Fe transporter to carry utilizable iron); and producing phytohormones, such as indole acetic acid, secreted effectors, and antibiotics to protect plants from pathogens. AHL, N-acyl homoserine lactone; QSM, quorum-sensing molecules; VOCs, volatile organic compounds; Fe, iron; Cd, cadmium; Zn, zinc.

FIGURE 3

Mechanism of SAR and ISR utilizing phytohormones for inducing defense responses upon microbial incidence. Systemic acquired resistance involves salicylic acid accumulation after perception of pathogen by plants (in red) and expression of pathogenesis-related proteins in resistant tissues (upper leaf with dark red border) for inducing defense actions, whereas in induced systemic resistance, nonpathogenic plant growth–promoting rhizobacteria enable defense responses via ethylene and jasmonic acid priming process. NPR1 is the positive regulator of salicylic acid in SAR and is also needed in downstream processes of ethylene signaling in ISR. SAR, systemic acquired resistance; ISR, induced systemic resistance; SA, salicylic acid; ET, ethylene; JA, jasmonic acid; PRs, pathogenesis related genes; PGPR, plant growth–promoting rhizobacteria; NPR1, non-expresser of PR genes.

FIGURE 4

Detailed flowchart-based methodology for (A) metagenomics and (B) amplicon sequencing methods.

FIGURE 5

Description of the process involved in screening microbial cultures for PGP traits and development of inoculant. PGP, plant growth–promoting traits; HCN, hydrogen cyanide; 2,4-DAPG, 2,4-diacetylphloroglucinol.