Exploration of Plant-Microbe Interactions for Sustainable Agriculture in CRISPR Era

Shelake, Rahul Mahadev; Pramanik, Dibyajyoti; Kim, Jae‐Yean

doi:10.3390/microorganisms7080269

Cited by 102 publications

(57 citation statements)

References 248 publications

(321 reference statements)

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“…These mutually beneficial interactions between two living organisms are often called symbiosis, which involve multidirectional changes in the genome, metabolism, and signaling network. However, plant-microbe interactions can be either beneficial or harmful to one another [106]. The most common study in the beneficial plant-microbe interaction comes from leguminous plants and one of the Rhizobia species.…”

Section: Pd-rlks Govern Plant Growth and Developmentmentioning

confidence: 99%

The Role of Plasmodesmata-Associated Receptor in Plant Development and Environmental Response

Iswanto

Lee

et al. 2020

Plants

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Over the last decade, plasmodesmata (PD) symplasmic nano-channels were reported to be involved in various cell biology activities to prop up within plant growth and development as well as environmental stresses. Indeed, this is highly influenced by their native structure, which is lined with the plasma membrane (PM), conferring a suitable biological landscape for numerous plant receptors that correspond to signaling pathways. However, there are more than six hundred members of Arabidopsis thaliana membrane-localized receptors and over one thousand receptors in rice have been identified, many of which are likely to respond to the external stimuli. This review focuses on the class of plasmodesmal-receptor like proteins (PD-RLPs)/plasmodesmal-receptor-like kinases (PD-RLKs) found in planta. We summarize and discuss the current knowledge regarding RLPs/RLKs that reside at PD–PM channels in response to plant growth, development, and stress adaptation.

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Section: Pd-rlks Govern Plant Growth and Developmentmentioning

confidence: 99%

The Role of Plasmodesmata-Associated Receptor in Plant Development and Environmental Response

Iswanto

Lee

et al. 2020

Plants

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“…There are a wide variety of ways that the use of transposon insertion sequencing techniques in bacteria could be expanded beyond these current applications to rapidly increase our understanding of bacterial functions relevant for plant growth promotion and agriculture. Bacterial growth in the rhizosphere is influenced by the soil type and structure, soil organic matter, macronutrient levels and moisture levels (Shelake et al, 2019). These physico-chemical properties of the soil can vary at the centimeter scale so a bacterial inoculum applied to a crop may encounter a wide range of these conditions (Fierer, 2017).…”

Section: Future Avenues To Explore With Transposon Insertion Sequencingmentioning

confidence: 99%

“…These physico-chemical properties of the soil can vary at the centimeter scale so a bacterial inoculum applied to a crop may encounter a wide range of these conditions (Fierer, 2017). Bacteria residing in the phyllosphere (above ground plant surfaces) have to be able to cope with widely fluctuating environmental conditions, including light levels, water availability, temperature and UV radiation (Shelake et al, 2019). Transposon insertion sequencing techniques could be applied to plant-associated bacteria to determine which genes are involved in fundamental processes required for living in these environments and what genetic factors make some bacteria highly successful at colonizing these environments.…”

Section: Future Avenues To Explore With Transposon Insertion Sequencingmentioning

confidence: 99%

“…However, this is currently difficult to achieve with only a limited understanding of microbial gene functions and their interactions with plants on a molecular level. An increasingly common approach when studying agricultural microbiota is to ascertain microbial community composition using metagenomics (Shelake et al, 2019). This allows for the collection of genetic information about more members of the community than just the microbes that are able to be cultivated (Levy et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

“…The combination of these issues results in the functions of many microbial genes remaining unknown or poorly understood (Van Opijnen and Camilli, 2012;Jarboe, 2018). This is currently limiting our understanding of the role many microbes play in agricultural and other systems and hampers interpretation of microbiome survey data and efforts to formulate optimal plant associated microbial communities (Shelake et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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Application of Transposon Insertion Sequencing to Agricultural Science

2020

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Many plant-associated bacteria have the ability to positively affect plant growth and there is growing interest in utilizing such bacteria in agricultural settings to reduce reliance on pesticides and fertilizers. However, our capacity to utilize microbes in this way is currently limited due to patchy understanding of bacterial-plant interactions at a molecular level. Traditional methods of studying molecular interactions have sought to characterize the function of one gene at a time, but the slow pace of this work means the functions of the vast majority of bacterial genes remain unknown or poorly understood. New approaches to improve and speed up investigations into the functions of bacterial genes in agricultural systems will facilitate efforts to optimize microbial communities and develop microbe-based products. Techniques enabling high-throughput gene functional analysis, such as transposon insertion sequencing analyses, have great potential to be widely applied to determine key aspects of plant-bacterial interactions. Transposon insertion sequencing combines saturation transposon mutagenesis and high-throughput sequencing to simultaneously investigate the function of all the nonessential genes in a bacterial genome. This technique can be used for both in vitro and in vivo studies to identify genes involved in microbe-plant interactions, stress tolerance and pathogen virulence. The information provided by such investigations will rapidly accelerate the rate of bacterial gene functional determination and provide insights into the genes and pathways that underlie biotic interactions, metabolism, and survival of agriculturally relevant bacteria. This knowledge could be used to select the most appropriate plant growth promoting bacteria for a specific set of conditions, formulating crop inoculants, or developing crop protection products. This review provides an overview of transposon insertion sequencing, outlines how this approach has been applied to study plant-associated bacteria, and proposes new applications of these techniques for the benefit of agriculture.

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