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Plant microbiome (or phytomicrobiome) engineering (PME) is an anticipated untapped alternative strategy that could be exploited for plant growth, health and productivity under different environmental conditions. It has been proven that the phytomicrobiome has crucial contributions to plant health, pathogen control and tolerance under drastic environmental (a)biotic constraints. Consistent with plant health and safety, in this article we address the fundamental role of plant microbiome and its insights in plant health and productivity. We also explore the potential of plant microbiome under environmental restrictions and the proposition of improving microbial functions that can be supportive for better plant growth and production. Understanding the crucial role of plant associated microbial communities, we propose how the associated microbial actions could be enhanced to improve plant growth-promoting mechanisms, with a particular emphasis on plant beneficial fungi. Additionally, we suggest the possible plant strategies to adapt to a harsh environment by manipulating plant microbiomes. However, our current understanding of the microbiome is still in its infancy, and the major perturbations, such as anthropocentric actions, are not fully understood. Therefore, this work highlights the importance of manipulating the beneficial plant microbiome to create more sustainable agriculture, particularly under different environmental stressors.

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.

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