Plant Microbiome Engineering: Hopes or Hypes

Abstract

Rhizosphere microbiome is a dynamic and complex zone of microbial communities. This complex plant-associated microbial community, usually regarded as the plant's second genome, plays a crucial role in plant health. It is unquestioned that plant microbiome collectively contributes to plant growth and fitness. It also provides a safeguard from plant pathogens, and induces tolerance in the host against abiotic stressors. The revolution in omics, gene-editing and sequencing tools have somehow led to unravel the compositions and latent interactions between plants and microbes. Similarly, besides standard practices, many biotechnological, (bio)chemical and ecological methods have also been proposed. Such platforms have been solely dedicated to engineer the complex microbiome by untangling the potential barriers, and to achieve better agriculture output. Yet, several limitations, for example, the biological obstacles, abiotic constraints and molecular tools that capably impact plant microbiome engineering and functionality, remained unaddressed problems. In this review, we provide a holistic overview of plant microbiome composition, complexities, and major challenges in plant microbiome engineering. Then, we unearthed all inevitable abiotic factors that serve as bottlenecks by discouraging plant microbiome engineering and functionality. Lastly, by exploring the inherent role of micro/macrofauna, we propose economic and eco-friendly strategies that could be harnessed sustainably and biotechnologically for resilient plant microbiome engineering.

Keywords: biotic and abiotic hurdles; complexity; microbiome engineering; plant microbiome; suppressive soil.

Figure 1

A holistic overview of plant microbiome composition, complexity, and diversity.

Figure 2

Schematic diagram showing the potential services and hurdles of the plant microbiome. The host plant encounters both beneficial and harmful components concomitantly. The below-ground complex ecosystem harbors biotic and abiotic compositions that significantly influence plant health and fitness. The host plant thrives in a healthy microbiome, contrary, it gets diseases in an unhealthy and imbalanced microbiome.

Figure 3

The diagrammatic illustration of suppressive soil microbiome origination and the underlying mechanism. The microbiota establishes the disease suppression soil microbiome by employing an array of direct and indirect mechanisms. Collectively, these diverse microbial communities perform significant beneficial activities that promote plant growth and suppress harmful pathogens functions. Suppressive soil microbiome could be harnessed for resilient microbiome engineering via screening and isolating the responsible candidates of disease suppressive soil. Development of synthetic communities from suppressive soil microbiome could be inoculated into a conducive soil microbiome against soil-borne disease.