Sustainable Agriculture through the Enhancement of Microbial Biocontrol Agents: Current Challenges and New Perspectives

Abstract

The future of pesticide usage in agriculture is uncertain due to its unsustainability, adverse environmental impacts, and its association in enhanced phytopathogen resistance. Hence, this situation urges the development of new sustainable practices in agriculture. A promising approach involves endophytes, which are non-pathogenic microorganisms inhabiting the interior parts of plants. However, due to the vast diversity and complexity of plant microbiomes, a major gap has formed with regards to endophytic research and its application in phytopathogen biocontrol. The gap has mainly been increasing due to the difficulty of isolating underrepresented endophytes and due to limitation of previous genetic tools availability to further research and understand plant-microbe interaction, endophytic biocontrol capabilities and their biocontrol compounds. This review highlights the current challenges being encountered in this research field. Additionally, the research advances through utilization of specialized techniques (CRISPR/Cas9 system, nanoparticles and multi-omics) are highlighted to assist in elucidating the mechanism revolving around plant-microbe interactions and to generate model systems demonstrating improved biocontrol capabilities of endophytes. The ultimate goal of this review is to provide improved approaches that could be implement in an array of microorganism that will enhance the phytopathogen biocontrol field in order to create a sustainable agricultural sector.

Tiny Giants Endophytes in Sustainable Agriculture: Trends and Prospects

“…Therefore, appropriate knowledge, accessibility, and regulation of endophyte application should lead to expanded utilization across various agricultural sectors promoting crop yield and protecting the environment. However, useful the applications are, the utilization of endophytes in agricultural production comes with its challenges [11,128]. They include inadequate understanding of the ecological roles of endophytes, insufficient commercial microbial inoculant stocks [129], and regulatory barriers [130].…”

“…Therefore, interdisciplinary efforts are imperative in advancing the endophyte research [131]. "Researchers studying endophytes face difficulty in isolating underrepresented endophytes due to the vast diversity of plant microbiomes [ 132], a tendency to focus on well-known models in plant-fungal-stress combinations rather than exploring less studied factors [133], and the need for novel approaches in genotyping and phenotyping to consider the plantendophyte holobiont for breeding programs" [134]. Additionally, one of the conditions for the development of breeding endophytes is the necessity for a new approach in genotyping and phenotyping that takes into account the plant-endophyte holobiont [135].…”

“…The release of some bioactive substances by them can both protect plants from diseases and promote plant growth once colonised in healthy plant tissues [6,[8][9][10]. Additionally, these microbes can offer enhanced drought, moisture, and salinity tolerances, making them very appropriate for farming on marginal terrains [11]. They produce phytohormones, physiologically active substances, and some enzymes that can improve plant health and, productivity [12].…”

The Mitigation of Phytopathogens in Wheat under Current and Future Climate Change Scenarios: Next-Generation Microbial Inoculants

“…Promising directions for the future of omic-based biological control strategies lie in harnessing the vast potential of these advanced technologies to further enhance and optimize the efficacy of BCAs in agriculture and pest management. Integrating genomics, transcriptomics, proteomics, and metabolomics approaches can provide a comprehensive understanding of the complex interactions between BCAs and their target pests or pathogens, leading to the discovery of novel bioactive compounds and mechanisms involved in biocontrol [100]. Omic tools can facilitate the identification of key genes and pathways involved in the production of biocontrol-related secondary metabolites, such as antibiotics and enzymes, which are crucial for inhibiting pathogen growth [100].…”

“…Integrating genomics, transcriptomics, proteomics, and metabolomics approaches can provide a comprehensive understanding of the complex interactions between BCAs and their target pests or pathogens, leading to the discovery of novel bioactive compounds and mechanisms involved in biocontrol [100]. Omic tools can facilitate the identification of key genes and pathways involved in the production of biocontrol-related secondary metabolites, such as antibiotics and enzymes, which are crucial for inhibiting pathogen growth [100]. For example, the research carried out by Villa Rodríguez et al [67], integrating genomic and metabolomic results from the effect of Bacillus cabrialesii TE3 T on Bipolaris Sorokiniana TPQ3, revealed that strain TE3 T contains the biosynthetic potential to produce wide spectrum antifungal and antibacterial metabolites, and determined that a lipopeptide complex of surfactin and fengycin homologs was responsible for antifungal activity exhibited by B. cabrialesii TE3 T against the studied phytopathogen.…”