The phytomicrobiome: solving plant stress tolerance under climate change

Abstract

With extraordinary global climate changes, increased episodes of extreme conditions result in continuous but complex interaction of environmental variables with plant life. Exploring natural phytomicrobiome species can provide a crucial resource of beneficial microbes that can improve plant growth and productivity through nutrient uptake, secondary metabolite production, and resistance against pathogenicity and abiotic stresses. The phytomicrobiome composition, diversity, and function strongly depend on the plant's genotype and climatic conditions. Currently, most studies have focused on elucidating microbial community abundance and diversity in the phytomicrobiome, covering bacterial communities. However, least is known about understanding the holistic phytomicrobiome composition and how they interact and function in stress conditions. This review identifies several gaps and essential questions that could enhance understanding of the complex interaction of microbiome, plant, and climate change. Utilizing eco-friendly approaches of naturally occurring synthetic microbial communities that enhance plant stress tolerance and leave fewer carbon-foot prints has been emphasized. However, understanding the mechanisms involved in stress signaling and responses by phytomicrobiome species under spatial and temporal climate changes is extremely important. Furthermore, the bacterial and fungal biome have been studied extensively, but the holistic interactome with archaea, viruses, oomycetes, protozoa, algae, and nematodes has seldom been studied. The inter-kingdom diversity, function, and potential role in improving environmental stress responses of plants are considerably important. In addition, much remains to be understood across organismal and ecosystem-level responses under dynamic and complex climate change conditions.

Keywords: abiotic stress; extreme environment; metagenome; phytomicrobiome; plant growth.

Figure 1

Climate change due to the emission of GHGs and resulting global temperature and rainfall patterns significantly impacts the plant’s photosynthesis, defenses, and yields. This drastically impacts soil health, microbial activities, nutrient mobilization, and uptake and secretion of signaling metabolites. Thus, impacting both the phyllosphere and rhizosphere parts of the plant life. Phytomicrobiome members (bacteria, fungi, protozoa, oomycetes, viruses, algae, and nematodes), on the other hand, drastically increase or decrease to respond to the change climatic changes (drought, heat, cold, flooding, salinity, etc.). The structure, diversity, and function significantly shift from higher to low or low to higher for specific phytomicrobiome players. For example, diversity can reduce from bacteria to viral species in a given phyllosphere and rhizosphere segment during abiotic stress. A similar perspective has been considered for the degree of function and diversity from nematodes to algae in soil systems alongside bacterial and fungal species during stress. The interactome of Abundance (A) vs. stress protection (S), function (F) vs. diversity (D), and genotype (G) vs. environment (condition C) is extremely complex and dynamic. Thus, the lack or abundance of a specific class of phytomicrobiome players can significantly impact a plant’s function and response to climatic stresses. (Created with BioRender.com).

Figure 2

The Phytomicrobiome responds to host plant growth and stress tolerance by producing several signaling molecules. These secretomes directly influence plant microbiome structure and diversity. Hence, each climate-induced stress factor would directly challenge the composition and function of core-microbiome species associated with a host. Microbiome members’ associated plant growth and stress aversion defenses impact critical aspects of plant life (growth, metabolism, resistance to stress, gene regulation, and biomass yield). This also impacts nutrient cycling, transport, mobilization, and translocation inside plant tissues during optimal or stressful conditions. The core-microbiome function drastically changes and shifts from the rhizosphere into the phyllosphere. (Created with BioRender.com).