The findings on the strategies employed by endophytic microbes have provided salient information to the researchers on the need to maximally explore them as bio-input in agricultural biotechnology. Biotic and abiotic factors are known to influence microbial recruitments from external plant environments into plant tissues. Endophytic microbes exhibit mutualism or antagonism association with host plants. The beneficial types contribute to plant growth and soil health, directly or indirectly. Strategies to enhance the use of endophytic microbes are desirable in modern agriculture, such that these microbes can be applied individually or combined as bioinoculants with bioprospecting in crop breeding systems. Scant information is available on the strategies for shaping the endophytic microbiome; hence, the need to unravel microbial strategies for yield enhancement and pathogen suppressiveness have become imperative. Therefore, this review focuses on the endophytic microbiome, mechanisms, factors influencing endophyte recruitment, and strategies for possible exploration as bioinoculants.

The abundance of nutrient accumulation in rhizosphere soils has placed the rhizosphere as an “epicenter” of bacterial concentrations. Nonetheless, over the years, little attention has been given to bacterial inoculants and soil-like substrates. The reason is that many farmers and experiments have focused on chemical fertilizers as an approach to improve plant growth and yield. Therefore, we focused on assessing the application of rhizosphere soil and its associated bacteria for biotechnological applications. This review has been structured into major subunits: rhizosphere soil as a treasure trove for bacterial community concentration, biodegradation of lignocellulose for biofuel production, rhizosphere soil and its bacteria as soil amendments, and the role of rhizosphere soil and its bacteria for bioremediation and biofiltration. Hence, the efficient use of rhizosphere soil and its bacteria in an environmentally friendly way can contribute to healthy and sustainable environments.

The plant microbiome is pivotal to sustainable agriculture and global food security, yet some challenges hinder fully harnessing it for field-scale impact. These challenges span measurement and integration, ecological predictability and translation across environments and seasons. Key obstacles include technical challenges, notably overcoming the limits of current sequencing for low-abundance taxa and whole-community coverage, integrating multi-omics data to uncover functional traits, addressing spatiotemporal variability in microbial dynamics, deciphering the interplay between plant genotypes and microbial communities, and enforcing standardized controls, metadata, depth targets and reproducible workflows. The rise of synthetic biology, omics tools, and artificial intelligence offers promising avenues for engineering plant–microbe interactions, yet their adoption requires regulatory, ethical, and scalability issues alongside clear economic viability for end-users and explicit accounting for evolutionary dynamics, including microbial adaptation and horizontal gene transfer to ensure durability. Furthermore, there is a need to translate research findings into field-ready applications that are validated across various soils, genotypes, and climates, while ensuring that advances benefit diverse regions through global, interdisciplinary collaboration, fair access, and benefit-sharing. Therefore, this review synthesizes current barriers and promising experimental and computational strategies to advance plant microbiome research. Consequently, a roadmap for fostering resilient, climate-smart, and resource-efficient agricultural systems focused on benchmarked, field-validated workflows is proposed.

Background: Climate change poses significant threats to global agriculture, intensifying the effects of biotic and abiotic stresses that reduce crop production and imperil food security. Bioinoculants, specifically arbuscular mycorrhizal fungi (AMF), plant growth-promoting rhizobacteria (PGPR), and other beneficial microbial consortia, offer potential, eco-friendly alternatives to traditional agrochemical fertilizers within the structure of climate-smart agriculture. Methods: This review explores the mechanisms through which bioinoculants promote plant adaptation and mitigate stress, including their roles in nutrient acquisition, antioxidant synthesis, modulation of phytohormones, and improvement of soil structure and health. Results: Diverse applications of bioinoculants are discussed, with emphasis on enhancing crop yield and resilience under various harsh climate conditions, including salinity, drought, and extreme temperatures. The review critically peruses the challenges and limitations of bioinoculant use, such as their interaction with the native soil microbial community, variable efficacy, formulation stability, and scalability. Conclusions: By synthesizing current advances and identifying knowledge gaps, this review provides a comprehensive evaluation of the potential and limitations of bioinoculants in advancing climate-smart agriculture and offers strategic insights for researchers, policy makers, and practitioners dedicated to the development of agricultural sustainability.

Sustainable production refers to the production that meets the needs of the present, without compromising the ability of future generations to meet their own needs. At global level and mainly across Nigeria, rice fields are considered as one of the most important sources of atmospheric concentration of two greenhouse gases, mainly anthropogenic methane (CH4) and nitrous oxide (N2O) emissions. These greenhouse gases (GHGs) are produced under anaerobic conditions, and their production has negative environmental and health implications. Additionally, the growing demand for rice across Nigeria exceeds supply, resulting in a rice deficit. To overcome this challenge, rice production should be increased, with so much regard to less GHG emission. Moving forward, understanding the determinate of farmers’ mitigation strategies to GHGs will definitely enhance effort made for farmers to continue to mitigate easily over-time. Incidentally, empirical study on the present discourse is relatively scanty, isolated, and devoid of in-depth and quantitative analyses. Most empirical studies did not pay close attention to the determinants of rice farmers’ decisions to mitigation options to GHGs. Studies on mitigation of GHGs at a farm or household level should rigorously examine the socioeconomic characteristics that influence farmers’ decisions to practice GHG mitigation or not. These create a gap in research and make it extremely difficult if not impossible for the governments/interest groups to know the method they can adopt in helping farmers mitigate the negative impact of GHG emission in rice production. It was against this backdrop that this study was systematically undertaken.