Application of CRISPR-Cas9 in plant-plant growth-promoting rhizobacteria interactions for next Green Revolution

Abstract

Agriculture's beginnings resulted in the domestication of numerous plant species as well as the use of natural resources. Food grain production took about 10,000 years to reach a billion tonnes in 1960, however, it took only 40 years to achieve 2 billion tonnes in year 2000. The creation of genetically modified crops, together with the use of enhanced agronomic practices, resulted in this remarkable increase, dubbed the "Green Revolution". Plants and bacteria that interact with each other in nature are co-evolving, according to Red Queen dynamics. Plant microorganisms, also known as plant microbiota, are an essential component of plant life. Plant-microbe (PM) interactions can be beneficial or harmful to hosts, depending on the health impact. The significance of microbiota in plant growth promotion (PGP) and stress resistance is well known. Our understanding of the community composition of the plant microbiome and important driving forces has advanced significantly. As a result, utilising the plant microbiota is a viable strategy for the next Green Revolution for meeting food demand. The utilisation of newer methods to understand essential genetic and molecular components of the multiple PM interactions is required for their application. The use of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-mediated genome editing (GE) techniques to investigate PM interactions is of tremendous interest. The implementation of GE techniques to boost the ability of microorganisms or plants for agronomic trait development will be enabled by a comprehensive understanding of PM interactions. This review focuses on using GE approaches to investigate the principles of PM interactions, disease resistance, PGP activity, and future implications in agriculture in plants or associated microbiota.

Keywords: CRISPR/Cas 9; Rhizobacteria.

Fig. 1

Graphs representing impact of Green Revolution on major staple cultivars over years with respect to yield and price. A Maize, B wheat, C rice. Adapted from Ritchie and Roser (2013), Roser and Ritchie (2013)

Fig. 2

Beneficial and harmful bacteria in phyllosphere and rhizosphere. The aerial and root part of the plant represents the phyllosphere and rhizosphere, respectively. The phyllosphere and rhizosphere produce a variety of secondary metabolites and exudates that operate as a defence mechanism for the plant against pathogenic microorganisms while also influencing the assembly of helpful bacteria by functioning as a chemoattractant which result in a healthier plant

Fig. 3

Factors influencing the microbial assembly for beneficial plant–microbe interactions. These include abiotic and biotic factors. Abiotic factors are associated with environmental factors, soil and others. Biotic factors include plant- and PGPR-associated factors

Fig. 4

The bulk soil microorganisms serve as “seed banks”, with varying genetic ability to digest, use, and metabolise various metabolite substrates. Two-component systems and QS are critical for both inter-microbial and intra-microbial communications, leading to colonisation and biofilm formation. Lytic enzymes, such as lysozymes or cell-wall destroying enzymes, facilitate entry into plant tissues. Symbionts, unlike infections, are thought to release minimal quantities of lytic enzymes, and type 3 and type 4 secretion systems that deliver effector proteins, avoiding stimulation of plant immune response leading to mutualism. This characteristic isolates them from pathogenic infection systems. Pattern triggered immunity (PTI) and viral dsRNA are stimulated in phase 1 to silence the viral RNA genes. In phase 2, the PTI and silencing is disrupted giving rise to 1st ETS. In phase 3 activated 1st ETI is an intensified variant of PTI that frequently overcomes the hypersensitive response and apoptosis. In phase 4, the pathogens try to recover the suppressed ETI by generating modified effector molecules, this gives rise to 2nd ETI. On the other side, ROS are also generated to trigger the defence actions followed by the production of PR (Pathogenesis Related) proteins that further promotes inhibitory immunological responses by directly acting on pathogens. [PTI + Silencing – ETS + ETI] determines the eventual amplitude of disease resistance or vulnerability. Adapted from Zvereva and Pooggin ; Singh et al. ; Trivedi et al.

Fig. 5

DNA repair mechanisms involved in gene editing. A a Repair by non-homologous end joining (NHEJ) is error-prone and influences integration by fixing two double strand breaks brought about by Cas nuclease directing and carrying donor DNA. b Targeted deletions can be made by repairing two double-strand breaks caused by nuclease targeting two genomic locations at the same time. B a The homology-directed repair (HDR) pathway for genome editing carries homology arms to the specific site using double-stranded donor templates. b- Genome altering using single stranded oligodeoxynucleotide (ssODN) is an alternative method. Silent mutations avoid resulting target site recognition by the nucleases. Adapted from Pickar-Oliver and Gersbach (2019)