CONCLUSION AND PERSPECTIVES
In conclusion, recent advances confirm that the soil microbiome is key to soil and plant health, as discussed above. It is perhaps not surprising that plant-microbe interactions have not been exploited for agricultural purposes ago, given the relatively poor indicators of success under field conditions. However, our understanding of the potential positive effects of PGPM has greatly increased in recent years, as has our knowledge of underpinning mechanisms, particularly the molecules involved in inter-organism communication. Thus, while there are substantial gaps in current knowledge, plant-microbe interactions are an attractive target for improving crop resilience and for achieving sustainable yields under unfavourable environmental conditions. Ultimately, the optimisation of plant-microbe interactions will be pivotal to strategies aimed at the long-term carbon sequestration in soils that is crucial to nature-based solutions to climate change. Microorganisms are at the core of the global carbon cycle, not least because they are responsible for more than 50% of annual CO2/methane transformations and contribute to almost 50% of the annual global CO2-sequestration. Engineering a more sustainable carbon cycle requires a detailed molecular mechanism-based understanding of the enzymes involved in CO2/methane interconversions. This essential knowledge is a prerequisite for viable microbe-based solutions to climate change.
Tailoring the soil microbiome to boost plant yield is currently restricted to agricultural practices and adding probiotic microbial consortia, largely because gene editing approaches are limited by societal acceptance. Ambitious objectives have been set in Europe and in other continents to ensure food sovereignty, while enhancing agricultural sustainability. Such targets have to incorporate climate change reliance traits, together with a much higher efficiency in the use of essential resources particularly water, and soil nutrients. An ultimate aim is to reduce reliance on fertilizers and plant protection products. It will not be possible to achieve these goals without a revolution in plant breeding that includes a continuous flow of innovation and technology transfer, incorporating new knowledge as it becomes available. This requires a substantial acceleration in the development of new plant varieties that have improved microbial associations, and so can use available resources much more efficiently, and are better adapted to climate change. The rapid introduction of such varieties will only be possible if breeders have access to all of the available tools and technologies, and crucially that Government registration and legislation accepts new genomic technologies that are at the heart of current accelerated breeding opportunities.
Nano-enabled approaches have the potential to overcome the limitations of traditional microbiome engineering, such as the absence of specificity in attaining targeted manipulation, collateral fatality to microbial diversity, and lack of reliable robust results (Fig. 4E) (Hussain et al., 2023; You, Kerner, Shanmugam, & Khodakovskaya, 2023). However, the application of novel nanomaterials still requires comprehensive profiling to evaluate long-term efficacy on plant productivity and ecosystem health (Ahmed, Noman, Gardea-Torresdey, White, & Li, 2023). To date, the beneficial actions of such approaches have been studied largely under controlled conditions and hence effective translation into the field is uncertain. The practical relevance of increasing mechanistic knowledge hence requires extensive study under field conditions, where environmental constraints influence to composition and effectiveness of plant/microbiome interactions. Such information is essential to understand how we might best apply inoculants to fields, which remains a significant challenge (Kaminsky et al. 2018). Nevertheless, the strategies discussed above have as yet untapped potential, and are particularly important in developing countries (Ashwathi, 2019).
Soil microbial communities are not constant and vary according to developmental stage, tissue type, and sampling time (Quiza et al., 2023). Our increasing knowledge of the leaf and root microbiomes has demonstrated the diversity of bacteria that are adapted for survival on, as well as within plants. The phyllosphere is a conducive niche for horizontal gene transfer (HGT) between epiphytic bacterial strains, the plant surface thus provides a niche for the evolution of new variants. Gaining a deeper understanding of this dynamic environment for gene exchange and the emergence of new strains, together with the exploitation of the remarkable genomic diversity within epiphytic populations, will help overcome current limitations in host-range specificity and allow potential jumping to other host plants. This together, with a better understanding of the plethora of signalling molecules including ROS (and associated redox post-translational modifications) that contribute to the dialogue between plants and microbes, will provide an improved road map for exploitation of the bi/tri/multi-partite interactions with beneficial microbes that will underpin sustainable next-generation agriculture.