Current Techniques to Study Beneficial Plant-Microbe Interactions

Abstract

Many different experimental approaches have been applied to elaborate and study the beneficial interactions between soil bacteria and plants. Some of these methods focus on changes to the plant and others are directed towards assessing the physiology and biochemistry of the beneficial plant growth-promoting bacteria (PGPB). Here, we provide an overview of some of the current techniques that have been employed to study the interaction of plants with PGPB. These techniques include the study of plant microbiomes; the use of DNA genome sequencing to understand the genes encoded by PGPB; the use of transcriptomics, proteomics, and metabolomics to study PGPB and plant gene expression; genome editing of PGPB; encapsulation of PGPB inoculants prior to their use to treat plants; imaging of plants and PGPB; PGPB nitrogenase assays; and the use of specialized growth chambers for growing and monitoring bacterially treated plants.

Recent Advances in the Bacterial Phytohormone Modulation of Plant Growth

“…However, one should ask how bacteria have co-evolved their hormone production and modulation systems, and how plants influence and regulate the synthesis of these bacterial hormones under different environmental conditions. This could be studied through -omic responses in both PGPB and in their associated plants [ 105 ]. In fact, it has recently been suggested that it is possible to infer causal relationships between plant microbiota, including plant growth modulating bacteria, and the desired phenotypes of plant crops [ 106 ].…”

Perspectives on the Use of Biopolymeric Matrices as Carriers for Plant-Growth Promoting Bacteria in Agricultural Systems

“…PGPB have been used as biofertilizers and biopesticides for decades, improving plant health and promoting plant growth while protecting them from biotic (plant pathogens, including fungi, bacteria, viruses, insects, and nematodes) and abiotic (drought, salinity, flooding, extreme temperatures, pH, light intensity, and the toxicity of accumulated heavy metals) stresses by several different mechanisms, modulating the plant metabolism at physiological, morphological, biochemical, and molecular levels. The most studied abiotic stress conditions are drought and salinity [ 3 , 4 , 10 , 11 , 13 , 24 , 25 , 26 , 27 ]. PGPB can positively affect plant development through direct or indirect mechanisms [ 13 , 24 , 25 , 26 , 28 , 29 ].…”

“…Several reviews have been published in the last few years, mostly concentrating on the mechanisms of action of PGPB and how these microorganisms act under different biotic and abiotic stress conditions [ 3 , 4 , 10 , 11 , 13 , 14 , 15 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 ]. Acinetobacter , Agrobacterium , Arthobacter , Azotobacter , Azospirillum , Bacillus , Bradyrhizobium, Burkholderia , Enterobacter , Erwinia , Frankia , Klebsiella , Micrococcus , Paenibacillus , Pseudomonas , Rhizobium , Serratia , and Thiobacillus are among the PGPB genera reported in the literature [ 13 , 15 , 23 , 24 , 26 , 36 , 37 , 38 ].…”

“…Within this context, the establishment of a sustainable agriculture production system must attend to the needs for improved crop productivity with the maintenance of soil fertility and ecosystem services to reach food security for the current and future generations. The use of plant-growth promoting bacteria (PGPB) as agricultural inputs can meet the requirements for sustainability as an eco-friendly alternative to the use of potentially deleterious chemical fertilizers, herbicides, fungicides, and insecticides, while improving plant productivity and health [ 4 , 9 , 10 , 11 , 12 , 13 , 14 ].…”

The Promises, Challenges, and Opportunities of Omics for Studying the Plant Holobiont

“…Today, there is an ever-growing list of revolutionary approaches with the suffix-omics [ 1 ] that extends beyond those derived from the central dogma, i.e., genomics, transcriptomics, proteomics, and metabolomics. The application of these technologies in plant sciences has transformed our understanding of plant–microbe interactions [ 2 ]. Since the publication of the Arabidopsis thaliana microbiome [ 3 ], providing our first detailed look at this complex microbial world, scientists around the world have revealed how plants and microbes have their own sophisticated communication networks and division of labor that is subject to selection in alternative environments [ 4 ].…”