Plants interact with diverse microbial populations in the ecosystem (Delaux et al., 2015). Microorganisms can colonize on plants’ surfaces or internal parts depending on the host genotype and the molecular signals released by plant roots. Microorganisms can colonize on plants’ surfaces or internal parts depending on the host genotype and the molecular signals released by plant roots. Endophytes are prokaryotic bacteria found within the healthy host tissue (Brader et al., 2014). Bacterial endophytes can benefit the host in several ways, such as biotic and abiotic stress resistance, increased availability of nutrients, degradation of toxic molecules, and production of phytohormones (Kandel et al., 2015).

Plant population dynamics have soil microbial intermediation. The plant has a microbial population in the phyllosphere, endophytes, or rhizospheric microbes. The ecology and phenotype of the plants can be affected by the influence of symbiotic microbes on the atmosphere and competition for soil resources.

The plant genotype affects the microbial make-up of the phyllosphere, rhizosphere, and endophytic microorganisms (Lynch et al., 2001). Although the precise method involves the plant-associated microorganisms and ecosystem function, the other specific mechanism is still unknown. Because they are co-evolved with bacteria, plants are immobile and need to control the results of their intricate interactions (Schnitzer and Klironomos, 2011). Different sorts of chemicals are continuously produced by plant roots, gathered, and secreted into the soil (Wood et al., 2012) known as the root exudates which contain enzymes, water, mucilage, H⁺ ions, and primary, secondary compounds made up of carbon (Singh, 2015). Every plant species’ rhizosphere is known to have a microorganism population that is 100 times higher than soil and is mostly controlled by compounds generated by roots (Jonkers et al., 2003; Bever, 2003). The favorable plant-soil microbial response enhances the microbial populations’ spatial spread (Schimel et al., 2007), while negative reaction results in plant replacement, which demands recolonization of locally specific roots (Bever et al., 2010; Pedrotti et al., 2013).

It has been proposed that endophytic bacteria vary from rhizobacteria in their genetic architecture, which may account for their capacity to colonise plant tissues internally. However, no specific gene or gene family has been found to explain the endophytic regime. In a 2014 study, the whole genomes of nine Proteobacteria were compared to identify a list of genes that may play a role in the endophytic activity. So yet, only a few of those genes have undergone experimental testing to determine whether they are involved in endophytic colonisation (Shen et al., 2013; Ouyabe et al., 2019). In this study, we have documented some mechanisms involved in plant endophyte interaction at the molecular level.

PGPEs enhance plant development through three interconnected mechanisms: phytostimulation, biofertilization, and biocontrol. Phytostimulation is the production of phytohormones for direct plant development (Vishwakarma et al., 2021). The amount of the plant hormone ethylene frequently declines as a result of the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase (Cruz Barrera et al., 2020). According to numerous studies, the pea plant and the pepper plant (Pseudomonas putida and Piper nigrum, respectively) both have bacterial endophytes that release ACC deaminase to aid plant growth (Ruduś et al, 2013). By controlling ethylene levels in plants, ACC deaminize production may minimize abiotic stress because an increase in ethylene can obstruct DNA synthesis, root and shoot growth, and cell division. However, the specific method for enhanced plant development is still unknown (González Candia, 2021). Bacterial strains also produced other hormones which include abscisic acid, indole-3-acetic acid, and jasmonic acid, to stimulate plant growth (Forchetti et al., 2007).The endophytes can enhance plant growth by increasing the availability of important nutrients known as bio-fertilization.

Nitrogen fixation is the most studied phenomenon of bio-fertilization which is the conversion of atmospheric nitrogen into ammonia (Mishra and Arora, 2016). Bacterial species like Azospirillum spp., Pantoea agglomerans, and Azoarcus spp. all are known to be involved in a substantial amount of nitrogen fixation in plant roots (Indiragandhi et al., 2008). Nonetheless, only 21 PGPEs can increase plant phosphorus availability by solubilizing phosphate. The metal cation linked to phosphorous is chelated as a result of the release of low molecular weight acids, making it more available to plants. The researchers have isolated, identified, and assessed the ability of Achromobacter xiloxidans and Bacillus pumilus to solubilize phosphate in sunflowers (Barrera et al., 2020). PGPEs were utilized to treat corn, lowering the quantity of artificial phosphorus fertilizer required while increasing yields by up to 50% (Cruz Barrera et al., 2019).

The protection of plants from phytopathogens and their growth promotion is known as biological control. Antibiotic and siderophores production are involved in biological control mechanisms. Siderophores like pyochelin and alicyclic acid and chelate iron are not directly involved in disease control due to their competition with pathogens for trace metals (Leopold, 1964). The disease can be suppressed in plants by antimicrobial metabolites secreted by bacterial endophytes such as 2,4-diacetylphloroglucinol (DAPG). Seed treatment of eggplant (Solanum melongena) with DAPG-producing bacterial endophytes reduced 70% of eggplant wilt caused by Ralstonia solanacearum (Rana et al., 2020a).

Burkholderia, Bacillus, Pseudomonas, Enterobacter, and Serratia are just a few of the bacterial endophyte strains that are successful at preventing the growth of pathogenic germs in both in vitro and in vivo settings (Khan and Doty, 2009). Aside from that, bacteria from the genera Bacillus, Enterobacter, Arthrobacter, Azotobacter, Isolptericola, Streptomyces, and Pseudomonas improved the crop’s stress resistance from heat, drought, and salt (Rana et al., 2020b; Khalil et al., 2021). The most important interaction between these endophytes and symbiotic plants allowed the plants to significantly increase their biomass and height while lowering stress. Although, it is not yet clear how bacterial endophytes lessen abiotic stress (Liu et al., 2014).

Plants usually take nutrients from the soil which constitutes a pool for microscopic life forms including bacteria, fungi, actinomycetes, algae, and protozoa. So, among them, the bacteria are the most common ones and have the maximum proportion in soil. The maximum number of bacteria present in the rhizosphere near the roots of plants is different from bulk soil (Luu et al., 2020). As these bacteria are present in more concentration in the soil so the bacteria may affect a plant through three different pathways (Edwards and Harding, 2004). PGPEs can promote plant growth directly by expediting the procurement of compounds or modifying levels of plant hormones and reducing the inhibitory effect of plant growth and pathogenicity by acting as biocontrol agents (Yan et al., 2019). The benefits provided by the endophytes to the host plants and their mechanisms are described in ( Table 1 ).

Throughout their lives, plants are exposed to harmful abiotic and biotic stresses. The damage that bacteria, fungi, viruses, nematodes, viroids, and insects do to plants is referred to as “biotic stress.” Rhizobacteria that promote plant growth by generating phytohormones or facilitating the uptake of particular nutrients might affect plant growth through biotic stress (Tiwari et al., 2020). However, PGPR reduces or even eliminate the negative impacts of plant pathogens. For example, Pseudomonas fluorescens produces 2,4-Diacetyl Phloroglucinol, which inhibits the development of pathogenic fungi in plants (Suslow and Schroth, 1982). Chitinase and laminarinase, two extracellular enzymes generated by P. stutzeri, caused the lysis of Fusarium solani mycelia and root rot (Cano-Salazar et al., 2011). During a seven-month field trial, the endophytic B. cenocepacia reduced the prevalence of fusarium wilt disease in banana plants by 3.4%, compared to 24.5% in untreated infected plants (Sapak et al., 2008). The antibiotic Pyrrolnitrin, which helps to reduce cotton damping off losses brought on by Rhizoctonia solani, was developed by several endophytic Pseudomonas fluorescens strains (Timper et al., 2009). Fusarium oxysporum, which was used as a bio-agent to create resistance in tomato plants, was successfully protected against P. fluorescens in flowering plants (Dudai, 2011). A bacteria that inhabit plant roots called Bacillus amyloliquefaciens has the power to control plant diseases and promote plant growth (Vardi et al., 2021).

In a study, it was discovered that bacterial endophytes shield cucumber plants from the cucumber anthracnose produced by Pseudomonas fluorescents (Akköprü et al., 2021). It was once believed that Achromobacter sp., Streptomyces sp., and Bacillus licheniformis were responsible for the foliar disease known as downy mildew. The downy mildew disease infestation level was lowered by Pseudoperonospora cubensis (Basu et al., 2022), which ultimately resulted in an increased yield.

The management of pests, which has become a challenge for most crops since pests have evolved a tolerance to pesticides, is another use for these endophytic bacteria (Deng et al., 2014). Entomopathogenic bacteria have been used to combat pests that are immune to insecticides ( Figure 3 ). A few fungi from the genera Podonectria, Verticillium, Hirsutella, Sphaerostilbe, Agerata, Metarhizium Aschersonia, and Myriangium are used for the biological management of pests. Brevibacillus laterosporus is effective against nematodes, Lepidoptera, Coleoptera, and toxic fungi in plants in addition to insects (Skinner et al., 2014).

In recent years, next-generation sequencing (NGS) techniques have been utilized to study the whole population of cultivable or non-cultivable bacteria inside plants, as well as their genomes. The interaction of host and bacterial endophytes has insightful concerns for the biological functioning of plants. As a result of interactions, rapid changes in host phenotype occurs also it is assumed as a driving force for the speciation and co-evolution of both the genetic system of host and bacteria (Fawcett, 1944). Though old genetic techniques to study plant-microbe interaction are less efficient, time-consuming, costly, and labor-intensive required a wide range of experiments and are usually limited to certain known genes (De Oliveira et al., 2004) in comparison to investigating the host-microbe interactions in molecular levels, it is needed to understand the phenotypic phenomena and genomics in depth. So the development of NGS technologies or metagenomic studies has provided the best way to understand the host-pathogen system. Through this technology, we can construct genome models of different organisms, which includes strains, their natural populations over time and their evolutionary histories (Navas et al., 2017; Sharma et al., 2021).

These complicated interactions can be analyzed and integrated by viewing plant microbiomes as a system. To better understand endophytism, contemporary genomic investigations incorporating metaomics and comparative studies can be quite beneficial (Dubey et al., 2020). A better understanding of endophyte interactions could be used to improve agricultural management by increasing plant development, biocontrol, and bioremediation (Alaimo et al., 2018). Some of the tools being utilized or that could be used to understand the link between plants and endophytes include genome sequencing, comparative genomics, microarray, next-generation sequencing, metagenomics, and metatranscriptomics (Dixit et al., 2022). To study endophytes and their apparent function in host plant ecology, contemporary methods and approaches need to be investigated (Gaiero et al., 2013).

Another way to identify the endophytic bacteria interact with the plant is to isolate the endophytic bacteria culture and then classify based on its phenotypic traits, and a few isolates from each category are identified further through partial sequencing of the 16S rRNA gene (Khare et al., 2018). The results of partial sequencing show that the isolates belonged to the genera Pseudomonas, Stenotrophomonas, Bacillus, Pantoea, and Serratia of bacteria (Liu et al, 2017>2552). These isolates are tested for their ability to produce siderophores, phosphate solubilization, atmospheric nitrogen fixation, protease, and hydrogen cyanide, as well as phytohormones like auxin and gibberellin (Eid et al., 2019). Auxin and gibberellin, two plant growth hormones, can be produced by all strains, though to varying degrees. Almost all strains could solubilize phosphate (Lata et al., 2019). The outcomes of protease, siderophore, and atmospheric nitrogen-fixing ability vary between strains. These findings provide information on the relationship between endophytic bacteria and their host plant (Vandana et al., 2021).

Furthermost genomic methods require recognition of variations among sequences within species or populations, like point mutations, Addition/deletions, and structural variations in structures (Bulgarelli et al., 2013).

Some of the bacterial endophytes or PGPR are commonly used to control different diseases and as biological control agents so nowadays most of the focus is the understanding of complex interactions and their mechanisms and outcome either beneficial or harmful. It is hard to find the exact mechanism of interaction among complex microbial populations residing in the soil and environment near to host. So that proper characterization and management strategies can be devised according to the current need of time. In recent time peoples are preferring organic food and disliked the use of fertilizers and chemicals in agriculture. As the world population is increasing and food shortage issues are raised, in the current situation food security is an important topic for debate. Hence bacterial endophytes can be used as an alternative to chemical fertilizers, nutrient sources, and biological control agents for various plant pathogens. Scientists are focusing on the use of these endophytes in the form of biopesticides, and biofertilizers with different trade names for the control of different diseases and sustainable agricultural systems. Although the application of these endophytes in combination may lead to the development of optimum PGPEs inoculants that robust, and slight variation of environmental factors will not affect the plant growth promotion.

SM, MN, MH, MS, and MA conceived and conceptualized the study. MAS, AS, MB provided materials and technical assistance. SM, MS wrote original draft. SS, MSH, MS and MT technically reviewed and finalized the draft. All authors contributed to the article and approved the submitted version.