**5. Plant growth–promoting microbes**

results showed the strong support for the hypothesis that niche differentiation was based on the structuring of the AM fungal community by soil pH [91]. Root secretion of phenolics was induced in Fe-deficient soil and altered the microbial community in the rhizosphere [92].

Soil microorganisms play a crucial role in plant growth and plant exudates. Microorganisms can affect exudation by affecting the permeability of root cells and root metabolism. Microorganisms can also absorb certain compounds in root exudates and excrete other compounds. Soil microbes can produce secondary metabolites that affect plant signaling and metabolism and can be considered as a "plant secondary genome" that provides plant hosts with microbe-derived compounds [93]. Some microbes and also some antibiotics (e.g., penicillin and polymyxin) increased the exudation of organic materials, altered cell permeability, and increased leakage [94, 95]. Soil microbes can also induce the exudation of phenolic com-

Plant and rhizosphere microbial diversity varies throughout the plant life cycle. The factors influencing the composition and diversity of the microbial community can be classified as four processes: dispersal, drift, speciation, and selection [97]. For seed plants, the life cycle begins with a seed. Seed dispersal is an important ecological process. Seeds carry associated microbes that originate from their parent and the environment, thereby increasing the microbial diversity in a new environment. Recent studies have suggested that bacterial seed coatings can protect against pathogens [98]. Microbial seed epiphytes have an advantage over soil bacteria during plant colonization. Seed coating methods are a major area of research, and numerous patents have been filed (i.e., approximately 4000 results were found by a Google patent search for the key word "microbial seed coating" [99]. After seed dispersal, during seed germination, seed-bone microbes might gain a competitive advantage over other microbes to colonize after germination, and opportunistic microbes from the surrounding soil might have access to a novel niche as the plant develops. Microbial diversity and the community dynamically change throughout the plant life cycle.

Plant microbiota forms a complex network. A wide range of studies has demonstrated that plant-associated microbes live either inside plant tissue or on the surface of plant organs such as the leaves and roots [100, 101]. Agler et al. characterized the microbiome of *A. thaliana* leaves [102]. Field experiments showed that both plant genotype and abiotic factors affected the microbiome composition. In addition, they observed that specific species (e.g., the plant pathogen *Albugo* and the fungus *Dioszegia*) significantly affected the microbial community structure. Agler used the term "microbial hubs" for the presence of these specific species, which were strongly interconnected with other species in the microbial network of the plants.

pounds for enhancing plant Fe absorption in low-Fe availability soil [96].

**4. Microbial community diversity and plant performances**

**4.1. Variation of microbial community in plant life cycle**

**4.2. Networking of plant-microbes (hub and edge microbes)**

*3.2.2.4. Microorganisms*

100 Plant Ecology - Traditional Approaches to Recent Trends

The soil constitutes a pool of microscopic life forms including bacteria, fungi, actinomycetes, protozoa, and algae, and of these, bacteria are by far the most common. The highest numbers of bacteria are found in the rhizosphere, the region around the plant roots, as differentiated from the bulk soil [103]. Regardless of the concentration of bacteria in the soil, the bacteria may affect a plant in one of three ways. From the perspective of the plant, the interaction between the soil bacteria and a plant may be beneficial, harmful, or neutral [104]. Plant growth-promoting bacteria (PGPB) include those that are free living, those that form specific symbiotic relationships with plants (e.g., *Rhizobia* spp. and *Frankia* spp.), bacterial endophytes that can colonize some, or a portion of a plant's interior tissues and cyanobacteria. PGPB can promote plant growth directly by facilitating the acquisition of compounds or modulating plant hormone levels and indirectly by reducing the inhibitory effect of pathogenicity and plant growth by acting as biocontrol agents [105].

### **5.1. PGPB and abiotic stress**

In nature, all living organisms are affected by environmental factors such as abiotic stress. Some plants have internal mechanisms to cope up with such stress, while others overcome. Abiotic stress factors include water deficit, excessive water, extreme temperatures, and salinity. The association of PGPB with certain plants can help the plants combat certain abiotic stresses and prevent the plants from dying. In the past decade, bacteria belonging to different genera including *Rhizobium*, *Bacillus*, *Pseudomonas*, *Pantoea*, *Paenibacillus*, *Burkholderia*, *Achromobacter*, *Azospirillum*, *Microbacterium*, *Methylobacterium*, *Variovorax*, and *Enterobacter* have been reported to endow host plants under different abiotic stress environments [106].

### *5.1.1. Cold stress*

Maize plants exposed to low temperatures show reduced shoot and root growth that has been attributed to severe oxidative damage induced by cold stress [107, 108]. Treatment with *Pseudomonas* sp. DSMZ 13134, *B. amyloliquefaciens* subsp. *plantarum*, *Bacillus* simplex strain R41 with micronutrients (Zn/Mn), or seaweed extracts proved to be beneficial cold stress protectant [109]. Inoculation of tomato seeds with plant growth–promoting psychrotolerant bacteria from the genera *Arthrobacter*, *Flavobacterium*, *Flavimonas*, *Pedobacter,* and *Pseudomonas* significantly improved plant height, root length, and membrane damage in leaf tissues as evidenced by electrolyte leakage and the malondialdehyde content [110]. A cold-tolerant PGPB *Methylobacterium phyllosphaerae* strain IARI-HHS2-67, isolated using a leaf imprinting method from phyllosphere of wheat (*Triticum aestivum* L.), showed improved survival, growth, and nutrient uptake compared to a noninoculated control at 60 days under low-temperature conditions [111]. The chilling resistance of grapevine plantlets was enhanced when inoculated with a plant growth–promoting rhizobacteria, *Burkholderia phytofirmans* strain PsJN. The root growth increased by 11.8- and 10.7-fold at 26 and 4°C, respectively, and plantlet biomass increased by 6- and 2.2-fold at 26 and 4°C, respectively [112].

### *5.1.2. Heat stress*

The effects of global warming in recent years can be felt with the increase in global temperature. A thermo tolerant plant growth–promoting *Pseudomonas putida* strain AKMP7 was proven to be beneficial for the growth of wheat (*Triticum* spp.) under heat stress [113]. The bacterium significantly increased the root and shoot length and dry biomass of wheat as compared to uninoculated plants. Inoculation improved the level of cellular metabolites and reduced the activity of several antioxidant enzymes and membrane injury. Sorghum seedlings showed enhanced tolerance to increased temperature with the association of *Pseudomonas* sp. strain AKM-P6 [114]. Inoculation induced the biosynthesis of high-molecular-weight proteins in the leaves at elevated temperatures, reduced membrane injury, and improved the levels of cellular metabolites such as proline, chlorophyll, sugars, amino acids, and proteins.

### *5.1.3. Salinity*

Approximately 20–50% of crop yields are lost to drought and high soil salinity [115]. The United Nations Population Fund estimates that the global human population may well reach 10 billion by 2050 (www.unfpa.org). Crop plants are very sensitive to soil salinity, and it is one of the harshest environmental factors that limits the productivity of crops. Plant-microbe associations have been found to be beneficial against abiotic salt stress in *Zea mays* upon coinoculation with Rhizobium, while Pseudomonas was correlated with decreased electrolyte leakage and the maintenance of leaf water content [116]. Salinity resistant *Pseudomonas fluorescens*, *P. aeruginosa*, and *P. stutzeri* ameliorated sodium chloride stress in tomato plants, and an increase in roots and length were observed [117]. Jha et al. demonstrated that the endophytic bacteria *Pseudomonas pseudoalcaligenes* induced the accumulation of higher concentrations of glycine betain-like compounds, leading to improved salinity stress tolerance in rice [118]. *Dietzia natronolimnaea,* a plant growth–promoting rhizobacteria, was seen to modulate a stress response gene, which led to the protection of wheat from salinity stress [119]. *Staphylococcus saprophyticus* ST1 and *Oceanobacillus profundus* Pmt2 inoculants were able to produce a biofilm and an extracellular EPS, thus helping *Lens esculenta* Var. Masoor-93 to cope with salt stress [120]. Salt-stressed *Arabidopsis* plants treated with volatile organic compounds (VOCs) from *B. amyloliquefaciens* GB03 showed higher biomass production and less Na<sup>+</sup> accumulation compared to salt-stressed plants without VOC treatment [121].

### *5.1.4. Water stress resistance*

R41 with micronutrients (Zn/Mn), or seaweed extracts proved to be beneficial cold stress protectant [109]. Inoculation of tomato seeds with plant growth–promoting psychrotolerant bacteria from the genera *Arthrobacter*, *Flavobacterium*, *Flavimonas*, *Pedobacter,* and *Pseudomonas* significantly improved plant height, root length, and membrane damage in leaf tissues as evidenced by electrolyte leakage and the malondialdehyde content [110]. A cold-tolerant PGPB *Methylobacterium phyllosphaerae* strain IARI-HHS2-67, isolated using a leaf imprinting method from phyllosphere of wheat (*Triticum aestivum* L.), showed improved survival, growth, and nutrient uptake compared to a noninoculated control at 60 days under low-temperature conditions [111]. The chilling resistance of grapevine plantlets was enhanced when inoculated with a plant growth–promoting rhizobacteria, *Burkholderia phytofirmans* strain PsJN. The root growth increased by 11.8- and 10.7-fold at 26 and 4°C, respectively, and plantlet biomass

The effects of global warming in recent years can be felt with the increase in global temperature. A thermo tolerant plant growth–promoting *Pseudomonas putida* strain AKMP7 was proven to be beneficial for the growth of wheat (*Triticum* spp.) under heat stress [113]. The bacterium significantly increased the root and shoot length and dry biomass of wheat as compared to uninoculated plants. Inoculation improved the level of cellular metabolites and reduced the activity of several antioxidant enzymes and membrane injury. Sorghum seedlings showed enhanced tolerance to increased temperature with the association of *Pseudomonas* sp. strain AKM-P6 [114]. Inoculation induced the biosynthesis of high-molecular-weight proteins in the leaves at elevated temperatures, reduced membrane injury, and improved the levels of

cellular metabolites such as proline, chlorophyll, sugars, amino acids, and proteins.

*B. amyloliquefaciens* GB03 showed higher biomass production and less Na<sup>+</sup>

pared to salt-stressed plants without VOC treatment [121].

Approximately 20–50% of crop yields are lost to drought and high soil salinity [115]. The United Nations Population Fund estimates that the global human population may well reach 10 billion by 2050 (www.unfpa.org). Crop plants are very sensitive to soil salinity, and it is one of the harshest environmental factors that limits the productivity of crops. Plant-microbe associations have been found to be beneficial against abiotic salt stress in *Zea mays* upon coinoculation with Rhizobium, while Pseudomonas was correlated with decreased electrolyte leakage and the maintenance of leaf water content [116]. Salinity resistant *Pseudomonas fluorescens*, *P. aeruginosa*, and *P. stutzeri* ameliorated sodium chloride stress in tomato plants, and an increase in roots and length were observed [117]. Jha et al. demonstrated that the endophytic bacteria *Pseudomonas pseudoalcaligenes* induced the accumulation of higher concentrations of glycine betain-like compounds, leading to improved salinity stress tolerance in rice [118]. *Dietzia natronolimnaea,* a plant growth–promoting rhizobacteria, was seen to modulate a stress response gene, which led to the protection of wheat from salinity stress [119]. *Staphylococcus saprophyticus* ST1 and *Oceanobacillus profundus* Pmt2 inoculants were able to produce a biofilm and an extracellular EPS, thus helping *Lens esculenta* Var. Masoor-93 to cope with salt stress [120]. Salt-stressed *Arabidopsis* plants treated with volatile organic compounds (VOCs) from

accumulation com-

increased by 6- and 2.2-fold at 26 and 4°C, respectively [112].

102 Plant Ecology - Traditional Approaches to Recent Trends

*5.1.2. Heat stress*

*5.1.3. Salinity*

Water scarcity constrains plant productivity, and more crop productivity is lost due to water scarcity than any other abiotic stresses [122]. *Achromobacter piechaudii* ARV8 reduced the production of ethylene by tomato seedlings following water stress, and ARV8 did not affect the reduction of the relative water content during water deprivation. ARV8 significantly improved the recovery of plants when watering was resumed [123]. Water stress resistance was enhanced in green gram when treated with *P. fluorescens* Pf1 compared to untreated plants. *P. fluorescens* Pf1 was also found to produce the enzyme catalase under stress conditions, which helped to detoxify the compounds accumulated in green gram during adverse conditions [124].

Heavy metals are defined as metals with a density higher than 5 g/cm<sup>3</sup> [125]. Heavy metals cause a significant decrease in plant growth and protein content at high concentrations. The most common heavy metal contaminants are Hg, Cd, Cr, Cu, Pb, and Zn [126]. All of these elements are toxic to crop plants at high tissue concentrations. Heavy metal toxicity in plants leads to the production of reactive oxygen species that block essential functional groups of biomolecules. This reaction has been noted in Hg and Cd toxicity and causes oxidative injury in plants. Increasing concentrations of Hg (5–20 mg/kg soil) in tomato plant showed deleterious effects on survival percentage, germination, flowering, pollen viability, and reduced plant height. *P. putida* enhanced the Cd uptake potential of *Eruca sativa* and favored healthy growth under Cd stress by increasing the shoot length up to 27%, the root length up to 32%, the wet weight up to 40%, the dry weight up to 22%, and the chlorophyll content up to 26% [127]. Canola seeds inoculated with *Kluyvera ascorbata* SUD165 and grown under gnotobiotic conditions in the presence of high concentrations of nickel chloride were partially protected against nickel toxicity because the bacteria could lower ethylene-induced stress due to nickel toxicity [128]. *Photobacterium halotolerans* MELD1 facilitated the phytoprotection of *Vigna Unguiculata Sesquipedalis* against Hg at a concentration of 25 ppm, thus increasing productivity as well as reducing the translocation of Hg to the bean pods [121]. A plant-microbe phytoremediation system was created with the combination of vetiver grass and the functional endophytic bacterium *Achromobacter xylosoxidans* F3B for the removal of toluene in Ho et al. [129]. It was observed that *A. xylosoxidans* F3B improved the degradation of toluene in vetiver, resulting in a decrease in phytotoxicity and a 30% reduction of evapotranspiration through the leaves. Another study conducted by Ho et al. [130] observed that when *A. xylosoxidans* strain F3B was inoculated in *A. thaliana*, it helped the plant tolerate a lethal concentration of catechol and phenol and enhanced the phytoremediation and phytoprotection of the plant.

### **5.2. PGPB against biotic stress**

Plants must withstand adverse abiotic and biotic stresses when they are sessile (**Figure. 2**). Biotic stress in plants mainly includes damage caused by other living organisms such as insects, bacteria, fungi, nematodes, viruses, viroids, and protists. Biotic stress by PGPR can affect plant growth in two different ways; by the direct promotion of plant growth by the production of phytohormones or by facilitating the uptake of certain nutrients [45]. The indirect promotion of plant growth occurs when PGPR lessens or prevents the deleterious effects of phytopathogens. *P. fluorescens* produces 2,4-diacetyl phloroglucinol, which inhibits the growth of phytopathogenic fungi [131]. Extracellular chitinase and laminarinase were

**Figure 2.** Factors affecting plant-microbe interactions.

produced by *P. stutzeri,* which caused the lysis of mycelia of *F. solani*, which causes root rot [132]. The endophytic *B. cenocepacia* 869T2 decreased the disease incidence of Fusarium wilt in treated banana plants to 3.4%, compared to 24.5% in noninoculated plants infected in a field test during a 7-month period [50]. The antibiotic Pyrrolnitrin, produced by *P. fluorescens* BL915 could prevent the damage from *Rhizoctonia solani* during the damping off of cotton plants [133].

Van Peer et al. [134] described a mechanism called "Induced Systemic Resistance" in carnation plants that were systematically protected by *P. fluorescens* strain WCS417r against *F. oxysporum* f. sp. *Dianthi* and by Ardebili et al. in tomato plants, in which *P. fluorescens* CHA0 protected against *F. oxysporum f.* sp. Lycopersici acted as a bio agent that induced resistance in tomato [135]. *B. amyloliquefaciens* strain FZB42, a plant root colonizing isolate, was seen to have the ability to stimulate plant growth and suppress plant pathogens [136]. In another study, endophytes were seen to protect cucumber plants against cucumber anthracnose induced by *P. fluorescens* strain 89B-61 [137] and *Achromobacter* sp. F2feb.44. *Streptomyces* sp. Zapt10, and *Bacillus licheniformis* AE6 were exploited to induce systemic resistance in cucumber against the foliar disease of downy mildew caused by the phytopathogen *Pseudoperonospora cubensis,* which enhanced yield [138].

Pest management has become an issue over time because more and more pests are becoming immune to pesticides. The global pesticide market is growing at a pace of 3.6% per year and is valued around \$47 billion [139]. Development of entomopathogenic bacteria for pest management has been a new approach to handle resilient pests. Species belonging to the genera *Aschersonia*, *Agerata*, *Verticillium*, *Sphaerostilbe*, *Podonectria*, *Myriangium*, *Hirsutella*, and *Metarhizium* [140] are fungal species involved in the biological control of pests. *Bacillus thuringiensis* is the most well-known *Bacillus* species on which the efforts of the scientific community and industry have been focused [141]. *Brevibacillus laterosporus* Laubach action has been reported to be effective against insects such as Coleoptera [142], Lepidoptera [143], nematodes [144, 145], and phytopathogenic fungi [146].
