Recent Developments in Systems Biology and Metabolic Engineering of Plant–Microbe Interactions

Abstract

Microorganisms play a crucial role in the sustainability of the various ecosystems. The characterization of various interactions between microorganisms and other biotic factors is a necessary footstep to understand the association and functions of microbial communities. Among the different microbial interactions in an ecosystem, plant–microbe interaction plays an important role to balance the ecosystem. The present review explores plant–microbe interactions using gene editing and system biology tools toward the comprehension in improvement of plant traits. Further, system biology tools like FBA (flux balance analysis), OptKnock, and constraint-based modeling helps in understanding such interactions as a whole. In addition, various gene editing tools have been summarized and a strategy has been hypothesized for the development of disease free plants. Furthermore, we have tried to summarize the predictions through data retrieved from various types of sources such as high throughput sequencing data (e.g., single nucleotide polymorphism detection, RNA-seq, proteomics) and metabolic models have been reconstructed from such sequences for species communities. It is well known fact that systems biology approaches and modeling of biological networks will enable us to learn the insight of such network and will also help further in understanding these interactions.

Below‐ground connections underlying above‐ground food production: a framework for optimising ecological connections in the rhizosphere

“…In addition to inoculation, mechanistic knowledge on links between plant traits and soil organismal networks could enable another promising approach for promoting soil organismal networks that deliver desirable functions (Kumar et al 2016). While there is accumulating evidence that plant traits, and in particular root traits, can predict soil faunal and microbial community structure and functioning (De Vries et al 2012b;Grigulis et al 2013;Legay et al 2016), there is only limited evidence that links plant traits to soil microbial networks.…”

Interdomain ecological networks between plants and microbes

“…Belowground microorganisms and their interactions to plants connect the two communities of aboveground and belowground world and contribute to community structure and plant health (Hassani, Duran, & Hacquard, 2018), attracting both botanists and microbiologists. The plant microbiome can be subdivided into several important regions, such as rhizosphere, phyllosphere and endosphere, due to their unique conditions present on and in different areas of plants (Bulgarelli, Schlaeppi, Spaepen, van Themaat, & Schulze-Lefert, 2013;Kumar, Baweja, Singh, & Shukla, 2016). The microorganisms living in these different spheres play important roles in plant nutrition acquisition, mutualistic defence and co-evolution (Fitzpatrick et al, 2018;Kenrick & Strullu-Derrien, 2014;Martin, Uroz, & Barker, 2017).…”

Catalytic Interactions and Molecular Docking of Bile Salt Hydrolase (BSH) from L. plantarum RYPR1 and Its Prebiotic Utilization

“…The interactions of probiotics with prebiotics have a beneficial role in improving the growth of normal microflora, resulting in immune system modulation of the host. A number of systems biology tools have been studied to comprehend the interactions between microorganisms and plant or human cell (Kumar et al, 2016). Furthermore, various genetic modifications which involve the introduction of desired genes may also have a constructive impact in the probiotic field (Gupta and Shukla, 2015).…”