Trends of Applied Microbiology for Sustainable Economy

Trends of Applied Microbiology for a Sustainable Economy discusses the role of modern tools and next-generation technologies in applied microbial research, including recent trends and innovation in global biofertilizers. Agriculture has seen dramatic changes since the time of its inception. Starting with the domestication of wild plants to small-scale traditional farming and then large-scale, chemical-intensive agriculture. It is at a crossroads once again, putting a huge amount of pressure on available natural resources like soil, water and biodiversity which is bound to increase with the ever-growing human population. This book helps readers understand the challenges associated with these demographic changes.

• Redefines the relationship between microorganisms and agricultural sustainability in view of the latest technologies and advancements
• Documents recent microbiological advancements in agricultural research and discusses challenges and opportunities in the biofertilizers market
• Identifies challenges and opportunities for scaling up biofertilizers technology
• Discusses recent trends and innovations in the biotechnology market and economy

• Language: English
• Publisher: Academic Press
• Release date: May 14, 2022
• ISBN: 9780323915960

Book preview

1: Trends of agricultural microbiology for sustainable crops production and economy: An introduction

Tanvir Kaur; Divjot Kour; Ajar Nath Yadav    Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India

Abstract

Microbes are organisms that are partner inhabitants of humans and other animals. They have been known to exist in various habitats including water, soil, air, and the interiors of animals as well as plants. These wonders have been known to perform several key roles such as decomposition and nutrient cycling. Their roles in the environment have got the limelight and many sectors are recognized where microbes can be used. Industries, agriculture, and environment are the three major sectors in which microbes can be utilized for various purposes. Agriculture is an important sector that feeds the worldwide population with several types of cereals and fruits. In the agriculture sector, different types of chemical inputs are applied to increase the yield and feed the growing population. Microbial-based inputs are a new trend that has been applied for quite a while now. Microbial-based inputs have been considered sustainable inputs that help in crop productivity. Microbes improve crop production by fulfilling the requirement of plants, along with protecting them from various biotic and abiotic stresses. This is an introductory chapter for the book Trends of Agricultural Microbiology for Sustainable Crops Production and Economy, which deals with the role of beneficial microbiomes for plant growth and plant protection for agricultural sustainability.

Keywords

Agriculture; Abiotic stress; Biotic stress; Crop production; Plant growth promotion; Sustainability

1.1: Introduction

A new trend in agriculture is the use of microbes for sustainable crop production. It is an alternative method for greener agriculture as conventional agricultural uses huge amounts of chemically synthesized products such as fertilizers and pesticides. The use of pesticides and fertilizers has been shown to impact the environment. The use of pesticides and fertilizers has adversely affected the quality of water as well as soil. Their use has also been proven to affect other organisms such as plants, small organisms, and microbial species. The use of microbes in agriculture has solved all related issues of the environment along with the farmer’s expectation of crop productivity (Kumar et al., 2021b).

Microbes undergo different types of mechanisms that help in increasing the growth, development, and productivity of the crop plant (Yadav, 2021a). The biological fixation of nitrogen; the solubilization of nutrients such as phosphorus, potassium, and zinc; the chelation of iron through the production of iron-chelating agents such as siderophores; and the production of phytohormones are some of the major mechanisms that help in directly promoting plant growth (Suman et al., 2016; Verma et al., 2017a; Yadav et al., 2018). These mechanisms are used to provide the entire basic growth nutrients that helps plants to develop such as nitrogen, phosphorus, potassium, and zinc. On the other hand, microbes also regulate agriculture productivity indirectly by protecting them from biotic and abiotic factors. Crop plants are host to many pathogens and pests that adversely affect productivity (Kaur et al., 2020b). Pests and pathogens, that is, biotic factors, affecting plant growth are serious destroyers of productivity. To control them, microbes are used to produce toxic compounds that inhibit pathogen growth (Singh et al., 2020c).

Ammonia, hydrogen cyanide, hydrolytic enzymes such as chitinase and β-1,3, and glucanase are some toxic compounds that inhibit pathogen growth and development. On the other hand, abiotic stress is also a major constraint that affects plant productivity. Drought, salinity, and extreme temperature are some abiotic stresses that affect crop growth. Such types of stresses in plant could be alleviated by the production of phytohormones and 1-aminocyclopropane-1-carboxylate deaminase (Verma et al., 2017b, c). All the above-mentioned microbial mechanisms play significant roles in plant growth and productivity and microbes can be applied as biofertilizer and biopesticides. Microbes as biofertilizers and biopesticides could also be used to conduct organic agriculture. Usually, organic agriculture is practiced without chemicals and only natural products are applied. Therefore, the use of these wonder organisms can also increase crop yield while leading to sustainable agriculture (Kour et al., 2019c).

Microbial products as biofertilizers and biopesticides are commonly available in the markets, which have been drastically increasing with the increase of environmental health awareness. Presently, in 24 countries, 170 organizations are involved in the production of commercial biofertilizers. This is an introductory chapter for the book Trends of Agricultural Microbiology for Sustainable Crops Production and Economy, which deals with the complete basic functions of microbes in agriculture to enhance crop productivity, including mechanisms and their applications as well as the effect on the worldwide economy.

1.2: Role of beneficial microbiomes in plant growth promotion

Beneficial microbes are ubiquitous in nature and have been sorted out as soil and plant microbiomes. These microbes have the capability to promote plants using diverse plant growth-promoting mechanisms while protecting the plant from phytopathogenic microbes and diverse abiotic stresses. They have been recognized as potential crop enhancers that increase crop productivity in a sustainable way by undergoing various mechanisms including nitrogen fixation; phosphorus, potassium, and zinc solubilization; and the production of siderophores, ammonia, HCN, and phytohormones (Kaur et al., 2021; Yadav, 2021b). The use of microbes as bioinoculants is a sustainable tool for agroenvironmental sustainability (Fig. 1.1).

Fig. 1.1

Fig. 1.1 A schematic representation for the characterization of microbes and their agricultural applications for sustainable development. Adapted with permission from Kour, D., Kaur, T., Devi, R., Rana, K.L., Yadav, N., Rastegari, A.A., et al., 2020a. Biotechnological applications of beneficial microbiomes for evergreen agriculture and human health. In: Rastegari, A.A., Yadav, A.N., Yadav, N. (Eds.) Trends of Microbial Biotechnology for Sustainable Agriculture and Biomedicine Systems: Perspectives for Human Health. Elsevier, Amsterdam, pp. 255–279. https://doi.org/10.1016/B978-0-12-820528-0.00019-3.

1.2.1: Nitrogen fixation

The most important constituent of living organisms (plants, animals, and microbes) is nitrogen. It is found in biological molecules such as amino acids and nucleic acids (RNA and DNA). On Earth, nitrogen is the most abundant element and is present as di‑nitrogen (N2) gas in the Earth’s atmosphere. However, the element is not available for the majority of organisms, especially plants and microbes, because of nitrogen molecule inertness (high strength of triple bound and stable electron configuration) (Valentine et al., 2018). As a result, modern agriculture is largely dependent upon chemically synthesized nitrogen fertilizer to meet nitrogen requirements and increase crop yields (Yadav, 2021c).

On the other hand, microbes, especially bacteria containing the nif gene (coding gene of nitrogenase, a protein complex), fix nitrogen via the ATP-dependent process of biological nitrogen fixation. Bacteria reduce the inert nitrogen gas molecules and convert it into simpler compounds such as ammonia and nitric oxide in the presence of protein complex, nitrogenase to fulfill its own nitrogen requirement (Dos Santos et al., 2012). In nature, three different types of bacteria are known to fix nitrogen: associative, free-living, and symbiotic (Mahmud et al., 2020) (Table 1.1). Free-living nitrogen-fixing bacteria exist in soil. Bacterial species such as Novosphingobium sp., Pseudomonas sp., Serratia sp. (Islam et al., 2013), Azotobacter vinelandi (Bellenger et al., 2011), Azotobacter chroococcum (Basak and Biswas, 2010), Paenibacillus riograndensis (Beneduzi et al., 2010), and Paenibacillus jilunlii (Jin et al., 2011) are some examples of free-living nitrogen-fixing bacteria.

Table 1.1

Symbiotic bacteria develop symbiotic relationships with leguminous plants by forming nodules with the help of a nod gene. Genera such as Rhizobium, Bradyrhizobium, Mesorhizobium, and Sinorhizobium, which are collectively known as rhizobia, are classified as symbiotic nitrogen-fixing bacteria (Mahmud et al., 2020). The third type of nitrogen-fixing bacteria, associative bacteria, is endophytic and fixes nitrogen. Pantoea agglomerans (Rana et al., 2021), Pseudomonas stutzeri (Pham et al., 2017a), and Gluconacetobacter diazotrophicus (Meneses et al., 2011) are some endophytic nitrogen-fixing bacteria.

In agriculture, these microbes could be used as potent nitrogen biofertilizers for the enhancement of sustainable plant growth yield while replacing chemical-based fertilizers (Farrar et al., 2014; Vandana et al., 2017). Much evidence is available showing that that these microbes enhance plant growth and promotion along with crop productivity. In the study from Basak and Biswas (2010), it was reported that the coinoculation of potassium (K) solubilizing and nitrogen (N) fixing bacteria, Bacillus mucilaginosus and A. chroococcum respectively, in Sudan grass (Sorghum vulgare) enhanced plant growth. It was reported that coinoculation also enhanced the biomass of the plant acquisition of nutrients and the K and N content in the soil. In a similar study, the coinoculation of phosphorus-solubilizing and N-fixing bacteria, identified as Pseudomonas chlororaphis and Arthrobacter pascens respectively, in walnut seedlings increased P and N uptake and biomass (Yu et al., 2012). In a report, the free-living nitrogen-fixing bacterium Novosphingobium sp. inoculated in red pepper roots significantly enhanced chlorophyll and the uptake of different macro- and micronutrients from the soil compared to noninoculated plants (Islam et al., 2013).

Another study reported four different species of dizaotrophic bacteria belonging to the genera Bacillus, Klebsiella, Microbacterium, and Paenibacillus that were reported to enhance the plant growth of rice seeds (Ji et al., 2014). An endophytic diazotroph of the lodgepole pine, Paenibacillus polymyxa, was reported as enhancing the plant growth of the gymnosperm tress species (Tang et al., 2017). In another study, the nitrogen-fixing and plant growth-promoting rhizobacterium P. stutzeri was reported to increase the plant growth of rice seedlings compared to chemically fertilized rice seedlings (Pham et al., 2017b). In a study, three different species belonging rice genera Sphingomonas, Psychrobacillus, and Enterobacter, namely Sphingomonas trueperi, Psychrobacillus psychrodurans and Enterobacter oryzae, were reported as significant fixers of biological nitrogen. The inoculation of these strains in maize and wheat plants was reported to promote early growth, root length, root structure, and nutrient uptake in maize as well as the dry weight of roots and the number of roots tips in wheat plants (Xu et al., 2018b). In a similar report, Pseudomonas stutzeri inoculated in maize was reported to improve plant growth by fixing nitrogen (Ke et al., 2019).

1.2.2: Phosphorus solubilization

Phosphorus is the second most required nutrient for structural and metabolic functions. It builds up about 0.2% of the dry weight of plants. This nutrient is a major component of nucleic acids and phospholipids and it is also involved in energy transfer mechanisms. In plants, it also helps in the formation and elongation of roots, along with tolerance to cold and diseases (Kour et al., 2021b). Phosphorus is the second mineral nutrient after nitrogen that is commonly a limiting factor for growth plant, as only 0.1% of the phosphorus is available for plant use (Zhu et al., 2011a). Traditionally, phosphorus deficiency is addressed through synthetically synthesized phosphorus fertilizer (diammonium phosphate and monoammonium phosphate). However, phosphorus-based fertilizers are not used by the plant completely, which causes environmental problems such as fertility loss and the contamination of soil and groundwater as well as eutrophication (Kang et al., 2011; Kumar et al., 2021; Kour et al., 2019b).

Various phosphorus-solubilizing microbes (PSB) are used to solubilize both P present in nature, that is, organic (Po), and the inorganic (Pi) form of phosphorus through different mechanisms (Kour et al., 2020d). The inorganic form of P is solubilized by the principle mechanism, that is, the production of mineral-dissolving compounds such as carbon dioxide, protons, organic acids, hydroxyl ions, and siderophores (Sharma et al., 2011). The solubilization of P via organic acid production is the well-known mechanism in which the P is released by lowering the soil pH (Usha and Padmavathi, 2012). The solubilization of the organic form of P, which is also referred to as phosphorus mineralization, is done through the enzymatic action of the enzyme phytase (Singh et al., 2020b). This enzyme mineralizes inositol phosphate (soil phytate), which is the most abundant form of organic P. These two mechanism of P solubilization and mineralization avail the phosphorus in soil which could be utilized by the plants for their development (Alori et al., 2017).

Therefore, the use of plant growth-promoting microbes is an efficient strategy for P supplementation to plants for their development. Several microbes such as actinomycetes, archaea, algae, bacteria, and fungi mineralize, solubilize, and mineralize the insoluble form (apatite, fluoroapatite, francolites, strengite, variscite, and wavellite) to the soluble form of P (H2PO4− and HPO4²   −). In a study, various bacterial isolates were sorted from the root-associated soil and the bulk soil of orchards. From all the bacterial isolates, 21 were reported as efficient solubilizers of phosphorus. Among all the isolates, Enterobacter aerogenes, Burkholderia spp., and Acinetobacter baumannii were reported as efficient solubilizers of tricalcium phosphate and recognized to promote the growth of Phaseolus vulgaris (Collavino et al., 2010). In another study, a halo-tolerant bacterium was reported for solubilizing phosphorus via organic acid production, namely Bacillus magaterium (Xiang et al., 2011).

In a similar report, the bacterium Pseudomonas aeruginosa and the fungus Aspergillus sp. were reported for solubilizing the inorganic form of phosphorus under saline conditions (Srinivasan et al., 2012). A thermo-tolerant bacterium, Brevibacillus sp., was also reported for solubilizing P (rock phosphate). This bacterium was reported for solubilizing P via acid production such as citric, gluconic, formic, and malic acid (Yadav et al., 2013). In another report, three potential phosphate-solubilizing bacteria, Acinetobacter pittii, Escherichia coli, and Enterobacter cloacae, isolated from the rhizosphere and the bulk soil of a field cultivated with betel nut were reported as an efficient mobilizer P nutrient (Liu et al., 2014). Archaea, unique microbes that inhabit places with extreme temperature, pH, and salinity, have also been reported for solubilizing phosphorus. In a report, haloarchaea isolated from the water, sediments, and rhizospheric soil of plants growing in the Rann of Kutch, Natrinema sp. and Halococcus hamelinensis, were reported as potential solubilizers of P. These archeal strains were reported for solubilizing phosphorus via lowering the soil pH through organic acid production (Yadav et al., 2015).

The fungal species Aspergillus niger and Penicillium oxalicum were also reported for solubilizing P. In this study, it was reported that both fungal strains were solubilizing phosphorus through the production of organic acids such as citric, formic, and oxalic acids (Li et al., 2016). A Gram-positive bacterium named Bacillus cereus, sorted out from Chinese cabbage root-associated soil, was reported as solubilizing P via the production of acetic, ascorbic, citric, lactic, and tartaric acids (Wang et al., 2017). In a report, phosphorus-solubilizing fungi identified as Aspergillus neoniger and Talaromyces aurantiacus isolated from the moso bamboo were reported as solubilizing P in acidic stress conditions (Zhang et al., 2018). In another report, drought stress-tolerant microbes were also reported for solubilizing P nutrients Pseudomonas libanensis (Kour et al., 2019a), Streptomyces laurentii, Penicillium sp. (Kour et al., 2020b), and Acinetobacter calcoaceticus (Kour et al., 2020c). Tsukamurella tyrosinosolvens, which was isolated from roots associated with the soil of tea, was also reported in a study for solubilizing phosphorus macronutrients (Zhang et al., 2021).

1.2.3: Potassium solubilization

Potassium (K) is another essential plant growth-promoting macronutrient. It the third most required nutrient of plants and in higher plants, it is the most abundantly absorbed cation. K plays an important role in plant growth, development, and metabolism. It is also used to activate several plant enzymes, increase photosynthesis, reduce respiration, maintain cell turgor, and help in the uptake and transportation of nitrogen and sugars. Moreover, potassium also plays a key role in crop quality as it helps increase disease resistance, grain filling, and kernel weight (Ahmad et al., 2016; Rajawat et al., 2020; Teotia et al., 2016). If plants don’t get the necessary amount of potassium, the plant may be poorly developed and its roots and seeds will be not developed, which may lead to lower crop productivity. In earlier times, the potassium in soil was rich. But now, the amount of K has been depleted due to the overexploitation of the land (Sindhu et al., 2014).

To fulfill the plant requirement of K, chemical fertilizer such as potash is being used, but it has various environmental issues. Agriculturally important microbes are also reported for solubilizing K in soil in insoluble form such as feldspars, muscovite, orthoclase, biotite, illite, vermiculite, micas, and smectite (Sparks and Huang, 1985). Various potassium-solubilizing microbes are known to solubilize the K in soil by different mechanisms. Acid production is a mechanism through which K can be solubilized. In acid production, microbes produce various types of organic acids such as citric, oxalic, and tartaric acids. The production of acidic compounds is the predominant mechanism of K solubilization. Another known mechanism of potassium solubilization through microbes is the production of exopolysaccharides. This mechanisms helps in releasing K from silicates as produced exopolysaccharides absorb SiO2 and lead to a reaction toward SiO2 and K+ solubilization (Sindhu et al., 2014).

Numerous microbes have been reported to solubilize K in soil through listed mechanisms. In a report, Paenibacillus glucanolyticus isolated from the black pepper rhizosphere was reported as a potential solubilizer of K in soil (Liu et al., 2012). Isolated bacteria from Iranian soil, identified as Bacillus megaterium and Arthrobacter sp., were also reported for K solubilization (Keshavarz Zarjani et al., 2013). In a similar report, KSB strains were isolated from the tobacco plant rhizosphere, namely Agrobacterium tumefaciens, Burkholderia cepacia, E. aerogenes, Klebsiella variicola, Microbacterium foliorum, and P. agglomerans. Among these strains, K. variicola was reported as a potential KSB and it also helped in the plant growth promotion of the tobacco plant (Zhang and Kong, 2014).

In a similar report, Frateuria aurantia was reported as a potential solubilizer of K; it also promotes tobacco plant growth after inoculation compared to a control (Subhashini, 2015). Pseudomonas azotoformans was also reported as an efficient solubilizer of K. This strain was also reported as degrading pollution and rejuvenating land for agriculture benefits (Saha et al., 2016a). In another report, three bacterial strains identified as Enterobacter sp., Pantoea ananatis, and Rahnella aquatilis, were reported for solubilizing both K and P via organic acid production. All these strains individually enhanced the plant growth, biomass, height, diameter, and leaf area of rice seedlings (Bakhshandeh et al., 2017). A. tumefaciens was recognized as a pronounced K solubilizer. The inoculation of this strain on maize also enhanced nutrient assimilation and plant growth (Meena et al., 2018). Bacillus pseudomycoides (Pramanik et al., 2019), A. pittii, Ochrobactrum ciceri (Ashfaq et al., 2020), and Burkholderia cenocepacia (Raji and Thangavelu, 2021) were also reported as potential solubilizers of K (Raji and Thangavelu, 2021).

1.2.4: Zinc solubilization

Zinc (Zn) solubilization is another mechanism through which agriculturally important microbes promote plant growth. Zinc is an essential nutrient required in minute concentrations for humans, animals, and plants. In plants, zinc plays a key role in photosynthesis; the metabolism of carbohydrates, auxins, and proteins; the formation of sucrose and starch; and reproduction (Saravanan et al., 2011). Plants absorb this nutrient in zinc ion (Zn²   +) form. In a soil solution, zinc ions are present in an insufficient amount as zinc is in the insoluble form. The insufficient supply of this nutrient could result in plant abnormalities that affect crop productivity (Hafeez et al., 2013; Sahu et al., 2018).

Plant growth-promoting microbes used to solubilize and mineralize these nutrients also help promote plant growth and development. The zinc-solubilizing microbes (ZSB) could convert the insoluble form of Zn to a soluble form through single and multiple mechanisms. Like other nutrient solubilizations, ZSB could solubilize insoluble zinc by producing organic acids such as 2-ketogluconic acid (Fasim et al., 2002) and 5-ketogluconic acid (Saravanan et al., 2007). The organic acid production helps in lowering pH and releases zincs ions. The other mechanism that solubilizes zinc is mineral chelation through zinc-chelating compounds released by microbes (Obrador et al., 2003). Chelation of zinc is the dominant process for zinc availability then organic acids production mechanism (Hussain et al., 2018).

Earth’s crust has abundant zinc solubilizers. Many studies have reported various microbial species for Zn solubilization. In a report, Bacillus aryabhattai was reported as an efficient solubilizer of zinc. The strains also exhibited other plant growth-promoting attributes such as IAA, ammonia, and siderophore-producing traits; they reportedly enhanced the yield of wheat and soybeans (Ramesh et al., 2014). In another investigation, the rhizobacteria of wheat and sugarcane were identified as potential zinc solubilizers, that is, E. cloacae, Pseudomonas fragi, Pantoea dispersa, and P. agglomerans. These strains also significantly increased zinc in wheat after inoculation compared to control (Kamran et al., 2017).

Other zinc-solubilizing bacteria were identified as Bacillus sp., B. substilis, and B. aryabhattai. These strains also contributed to increasing the maize root and shoot length as well as the biomass (Mumtaz et al., 2017). B. cepacia, Klebsiella pneumoniae, and P. aeruginosa were reported as potential zinc solubilizers (Gontia-Mishra et al., 2017). In another report, different strains of A. tumefaciens and Rhizobium sp. were also reported as solubilizers of zinc in a study by Khanghahi et al. (2018). Microbes such as B. megaterium (Dinesh et al., 2018; Bhatt and Maheshwari, 2020), Pseudomonas sp. (Zaheer et al., 2019), Bacillus sp., (Mumtaz et al., 2017; Ahmad et al., 2021), A. baumannii, and B. cepacia (Upadhyay et al., 2021) were also reported as efficient solubilizers of zinc; they were isolated from different soils including bulk and rhizospheric.

1.2.5: Siderophore production

Siderophore production is the plant growth-promoting mechanism of microbes that helps in the acquisition of iron nutrients from the soil. These are the small organic compounds produced under the iron-limiting conditions by plant growth-promoting microbes. Siderophores, a metal-chelating agent, have a high affinity toward ferric ions. Microbes use to produce these compounds for their own survival in iron depleted environment as iron plays a key role in electron transport chain, oxidative phosphorylation and tri-carboxylic acid cycles. Iron (Fe) is also an important nutrients for plants as it plays an important role in photosynthesis, oxidation–reduction reaction, biosynthesis of vitamins, antibiotics, toxins, cytochromes, nucleic acid pigments, and aromatic compounds (Fardeau et al., 2011; Messenger and Barclay, 1983). In soil, iron is a limiting factor that cannot be uptaken by plants, so microbes are used for iron acquisition through siderophore production.

Microbes produce three different categories of siderophores: catecholates, carboxylates, and hydroxamates (Saha et al., 2016b). These types of siderophores vary on the oxygen ligand for Fe(III) coordination. Hydroxamate siderophores are the most common type of siderophore in nature. This type of siderophore is usually produced by bacteria, and even fungi. This type of siderophore consists of C( glyph_dbnd O)N glyph_sbnd (OH) R, where R could be an amino acid or its derivative. Hydroxamates have the capability to form an octahedral complex with Fe³   +. The hydroxamates form a strong bond with ferric ions, which prevents hydrolysis and enzymatic degradation in the natural environment (Winkelmann, 2007). Another type of siderophore, catecholate, is mostly produced by bacteria. In this type of siderophores form a hexadentate octahedral complex by chelating iron with two oxygen atoms. Carboxylate siderophores are produced mostly by bacteria such as Staphylococcus and Rhizobium and fungi such as mucorales. Carboxylate siderophores form bonds with iron through carboxyl and hydroxyl groups (Dave and Dube, 2000).

Siderophore-producing capability has been reported by various microbial species such as Paracoccus sphaerophysae, an endophyte of the root nodule of Sphaerophysa salsalu. Additionally, this strain also shows antifungal activity (Deng et al., 2011). In another report, a species of the genera Streptomyces was reported as a producer of siderophores and auxin. The strain inoculated on wheat plants also enhanced the shoot length, dry weight, and nutrient concentration of nitrogen, phosphorus, iron, and manganese compared to the control (Sadeghi et al., 2012). Another investigation reported Bacillus amyloliquefaciens as a potent strain for producing siderophores which exquisite iron from soil. B. amyloliquefaciens has also been found to remediate soil contaminated with metals such as arsenic, lead, aluminum, and cadmium (Gaonkar and Bhosle, 2013). Siderophore production also has another benefits for plants in addition to iron availability, that is, pest biocontrol. The iron deficiency in soil also helps in killing pathogens and pests of plants. It was reported that a siderophore-producing bacteria, Pseudomonas sp., has been an antagonist against the pathogenic fungi Rhizoctonia solani (Solanki et al., 2014).

In a similar report, a pronounced producer of siderophores, the bacteria B. cepacia, was reported as an efficient biocontrol agent of pathogens such as Staphylococcus aureus and Enterococcus faecalis (Ong et al., 2016). In a report, two bacteria produced the hydroxamate type of siderophore, which helps in the acquisition of iron from soil (Ghavami et al., 2017). In another report, the siderophore-producing bacteria Aneurinibacillus aneurinilyticus, Aeromonas sp., and Pseudomonas sp. were reported to enhance plant growth when inoculated as a consortium by inhibiting the phytopathogen Fusarium solani (Kumar et al., 2018). In another investigation, microbial species such as Enterococcus casseliflavus, Pseudomonas weihenstephanensis, and Psychrobacter piscatorii reportedly produced siderophores (Sinha et al., 2019). Microbial species such as Bacillus halotolerans, Bacillus subtilis, Bacillus safensis (Sarwar et al., 2020), and Sinorhizobium meliloti were also reported as efficient producers of siderophores (Sepehri and Khatabi, 2021).

1.2.6: Phytohormone production

Plant growth and development are dependent on mineral nutrients, whether macro- or micronutrients. Along with nutrients, they also require phytohormones for their proliferation and development. Plants require phytohormones such as auxin, abscisic acid, cytokinin, ethylene, and gibberellins, which play various roles in plant systems (Tiwari et al., 2020). Auxin is an important class of phytohormones that plays a significant role in the regulation of various processes related to plant growth. Generally, auxins are synthesized by the plants at the root, shoot, and expanding leaves. Auxins are transported across the plant from the site of biosynthesis via auxin transporters. They are used to regulate other hormones such as strigolactones, which help maintain the organ founder cell population and trigger organ primordia initiation. They also play an important cellular role in the induction of CycD3 and CDKs, which govern various cell cycle checkpoints. Another important plant hormone, cytokinin, also plays a role in plant cell division activation and the regulation of the cellular level. Cytokinins also have an important role in the phosphoregulation of CDK at the G2/M checkpoint. These phytohormones are also the main driver of zeatin and chlorphyll production, leaf expansion, nutrition signaling, and root growth.

Gibberellins are another important phytohormone produced by microbes. This phytohormone helps in cellular elongation and division in plants. It also helps in internodium elongation (Davies, 2004). Similarly, abscisic acid also helps in the physiological functioning of plants under stress conditions (Rai et al., 2011). Ethylene is another important phytohormone of plants that helps in plant sharpening. Further, it regulates floral transition and root architecture (Vandenbussche and Van Der Straeten, 2018). All these phytohormones are usually synthesized by the plant itself, but in some harsh conditions, plants are not able to produce phytohormones. Microbes are also helpful in plant growth promotion by producing several types of plant growth hormones. They are reported for producing all five types of phytohormones required for plant development.

In a study, Acetebacter diazotrophicus from sugarcane was reported for the production of indole 3-acetic acid (IAA) (Patil et al., 2011). In another investigation, an epiphytic pink-pigmented methylotrophic bacterium, Methylobacterium sp., was isolated from different crops such as sugarcane, pigeonpea, potato, radish, and mustard. This strain was reported for producing cytokinin and its inoculation in wheat crops improves the seed germination, growth, and productivity of plants (Meena et al., 2012). In another study, a plant growt-promoting rhizobacteria was isolated from soil. It was identified as Promicromononspora sp. and was reported for secreting gibberellins. The inoculation of this strain on tomatoes enhanced crop production and salicylic acid (Kang et al., 2012). B. subtilis was reported for producing cytokinin and its inoculation in Platycladus orientalis (oriental thuja) seedlings under drought conditions increased organic acid production and alleviated drought stress (Liu et al., 2013).

The indole acetic acid type of phytohormone-producing bacterium called Planomicrobium chinense was isolated from a site contaminated with diesel oil; it was reported to enhance the growth of Vigna radiata (Das and Tiwary, 2014). In a similar report, the rhizobacteria of Panax ginseng, Pseudomonas fluorescence, and A. chroococcum, were also reported for producing IAA; they were also reported as potent species for the development of biofertilizer (Hussein and Joo, 2015). In another investigation, Lysinibacillus endophyticus, an endophytic bacterium isolated from corn root, was also reported for the production of indole-3-acetic (Yu et al., 2016). An endophytic fungus, Porostereum spadiceum, was reported for producing gibberellins; it also enhance soybean growth under salt stress (Hamayun et al., 2017b). In a report, two different species—B. subtilis and Azospirillum brasilens-were reported for the production of the phytohormone abscisic acid. These strains also help in alleviating heavy metal stress and their uptake through plant roots (Xu et al., 2018c).

In a study, Streptomyces fradiae was determined to be an efficient producer of IAA. The strain inoculation on tomato plant enhanced the root and shoot weight and length. Additionally, this strain increased the plant growth parameters almost two-fold compared to the control (Myo et al., 2019). An indole acetic acid-producing bacterium named Providencia sp. was sorted out from the rhizospheric region of the tomato. This bacterium also helps in promoting plant growth after inoculation (Rushabh et al., 2020). In another report, the rhizobacterium Pseudomonas koreensis, was reported for the production of gibberellins while also enhancing the growth of lettuce and Chinese cabbage (Kang et al., 2021).

1.3: Microbiomes for mitigation of biotic and abiotic stresses

Agricultural productivity is regulated by two major constituents: abiotic and biotic factors. The major abiotic factors affecting crop productivity include stress alkalinity, drought, flooding, salinity, and high and low temperatures (Kumar et al., 2019a, b). The biotic factors include pathogenic attacks, which have been known to account for about a 30% reduction in annual agricultural productivity (Fisher et al., 2012). There are a number of biotechnological tools that have been expansively applied to improve crops under stress conditions. Among these, the exploitation of plant growth-promoting microbes is of chief importance for their imminent role (Bhardwaj et al., 2014; Gangwar et al., 2017; Yang et al., 2009). Environmentally friendly approaches instigate a broad range of microbes for the promotion of plant growth, the improved uptake of nutrients, and tolerance to biotic and abiotic stresses. Inoculating crops with stress-tolerant, plant growth-promoting microbes is an effectual as well as novel way to alleviate stress conditions. This section deals with diverse stresses to which the plants are exposed and how stress-tolerant, plant growth-promoting microbes mitigate the adverse affects of abiotic stress.

1.3.1: Abiotic stress management

1.3.1.1: Salinity stress

Soil salinity is a major problem as far as soil health is concerned and is in fact increasing day by day, especially in arid and semiarid areas (Al-Karaki, 2006; Giri et al., 2003). According to FAO 2008 data, it was estimated that more than 800 million hectares of land throughout the world are affected by salinity (Munns and Tester, 2008). The major reasons for salinity include natural causes as well as the accumulation of salts for longer periods of time where evaporation greatly exceeds precipitation and salts dissolved in groundwater reach and accumulate at the soil surface through capillary movement (Estrada et al., 2013; Kohler et al., 2007). This stress is one of the major constraints limiting crop productivit. The development of salt-tolerant crop varieties could be one alternative, but the strategy is not economical for sustainable agriculture. However, inoculating crops with PGP microbes would be a better choice, as it minimizes production costs and environmental hazards (Arora et al., 2012). Upadhyay et al. (2012) showed the plant growth promotion and antioxidant activity of wheat with an inoculation of Arthrobacter sp. and B. subtilis under saline conditions. Ahmad et al. (2015) investigated Trichoderma harzianum’s role in mitigating the effect of salinity stress in Indian mustard. The treated seedlings showed enhanced shoot and root length, plant dry weight, proline content, oil content, and enzymatic activities as well as reduced malondialdehyde content. Metwali et al. (2015) reported the alleviation of salinity stress in the faba bean with an inoculation of B. subtilis, Pseudomonas fluorescens, and Pseudomonas putida.

Zhang et al. (2016) evaluated the role of Trichoderma longibrachiatum on wheat growth under salinity stress. The strain increased the relative water content in the roots and leaves, the chlorophyll content, the root activity, the leaf proline content, and antioxidant enzyme activity while decreasing the leaf malondialdehyde content under saline conditions. Hamayun et al. (2017a) evaluated the potential of a novel gibberellin-producing basidiomycetous endophytic fungus, P. spadiceum, to alleviate salinity stress and promote the health benefits of soybeans. Kumar et al. (2017) evaluated the role of salt-tolerant Trichoderma sp. on the growth of maize under salinity stress. The study clearly revealed the increase in shoot and root length, leaf area, total biomass, stem and leaf fresh weight, total chlorophyll, and proline and phenol content as well as a lower accumulation of malondialdehyde content. Wang et al. (2018) examined the effects of colonization with two AMF, Funneliformis mosseae and Diversispora versiformis, alone and in combination on the growth and nutrient uptake of Chrysanthemum morifolium in a greenhouse experiment under salinity stress. The study revealed that the root length, dry weight of the shoot and root, and root N concentration were higher in the mycorrhizal plants under conditions of moderate salinity, especially with the colonization of D. versiformis.

Xu et al. (2018a), studied the influence of Glomus tortuosum on the morphology, photosynthetic pigments, chlorophyll fluorescence, photosynthetic capacity, and rubisco activity of maize under saline stress in a pot experiment. The study validated that maize plants appeared to have a high dependency on AMF, which improved physiological mechanisms by raising the chlorophyll content, efficiency of light energy utilization, gas exchange, and rubisco activity under salinity stress. Kouadria et al. (2018), examined the roles of Alternaria chlamydospora, Chaetomium coarctatum, Embellisi aphragmospora, Fusarium graminearum, Fusariume quseti, and Phoma betae for their capability to improve the germination of durum wheat under salinity stress. Fungal strains considerably enhanced the germination and growth of durum wheat, with the highest germination percentage being shown by A. chlamydospora.Asaf et al. (2018) evaluated the potential of Aspergillus flavus to promote the growth of soybeans under salinity stress. The strain appreciably increased the growth of plants and mitigated salinity stress by downregulating abscissic acid and jasmonic acid while elevating antioxidant activities.

A study from Cordero et al. (2018) suggested PGPR as a viable, economical, and ecofriendly alternative to chemical fertilization in salinity soils. Vimal et al. (2019) reported the potential of Curtobacterium albidum in the alleviation of salinity stress in paddies. Nawaz et al. (2020) showed improved yield and growth in wheat with single as well as coinoculation of Bacillus pumilus, Exiguobacterium aurantiacum, and P. fluorescence under saline conditions. Sapre et al. (2021) reported the amelioration of salinity stress in peas with treatment of Acinetobacter bereziniae, Alcaligenes faecalis, and Enterobacter ludwigii. The utilization of PGP microbes in the alleviation of salinity stress is gaining worldwide interest and is a feasible option to maintain crop productivity under salinity conditions.

1.3.1.2: Drought stress

Drought stress is another major abiotic stress that causes a considerable decline in the yield and growth of most plants. Drought occurs slowly and silently and does not cause any prior short-term impact. This makes it harder for timely detection and preparation (Kerry et al., 2018; Sena et al., 2017). This situation is rapidly worsening by the widespread use of nondegrading chemical fertilizers, overgrazing, the overuse of land, and unsustainable exploitation of natural resources (Ruggiero et al., 2017). The deficiency of water greatly influences crop yield but improved yield under water-fed conditions is very important for food security (Ergen and Budak, 2009; Khan et al., 2018). Drought stress critically affects biochemical mechanisms and photosynthetic pigments, ultimately reducing crop growth and productivity (Moghadam et al., 2011). When plants are exposed to water-deficit conditions, reactive oxygen species (ROS) such as superoxides, hydrogen peroxide, and hydroxyl radicals accumulate (Chen et al., 2011). ROS are cytotoxic for cells and have an effect on proteins, nucleic acids, and lipids of the cell; they also stop the natural metabolism when present in high concentrations (Muthukumar et al., 2001). The application of PGP microbes is a strategy to mitigate drought stress and improve plant growth.

Sohrabi et al. (2012) investigated the effects of Glomus sp. on the physiological characteristics of the chickpea under nonstress as well as drought conditions. The inoculation of chickpea by arbuscular mycorrhizal (AM) considerably increased guaiacol peroxidases and polyphenol oxidase activities compared with the noninoculated chickpea. In general, the most guaiacol peroxidase and polyphenol oxidase activities were observed in plants inoculated with Glomus etunicatum and Glomus versiform species, and the most ascorbate peroxidase activity was observed in plants inoculated with Glomus intraradices. Shukla et al. (2012) studied the effect of drought-tolerant isolates of the endophytic fungus T. harzianum on rice. Rice seedlings colonized with Trichoderma were slower to wilt in response to drought. Drought conditions varying from 3 to 9 days of water holding increased the concentration of stress-induced metabolites in rice leaves. Zhu et al. (2012) studied the influence of AM fungus on growth, gas exchange, chlorophyll concentration, chlorophyll fluorescence, and water status of maize in pot culture under well-watered and drought stress conditions. AM symbioses remarkably increased the net photosynthetic rate and transpiration rate. Mycorrhizal plants had higher chlorophyll content, stomatal conductance, maximal fluorescence, maximum quantum efficiency of PSII photochemistry and potential photochemical efficiency, higher relative water content, and water use efficiency under drought stress when compared with nonmycorrhizal plants. Habibzadeh et al. (2013) evaluated the effects of the inoculation of Glomus mosseae and G. intraradices and water-deficit stress on mung plants. The inoculation improved the yield, leaf P and N, protein percentage, harvest index of protein, protein yield, seed yield, and ecosystem water use. The study suggested that both G. mosseae and G. intraradices appreciably improved the yield and reduced the water-deficit stress in mung bean plants.

Yaghoubian et al. (2014) investigated the effects of G. mosseae and Piriformospora indica on lipid peroxidation, antioxidant enzyme activity, and growth of Triticum aestivum under drought stress in a greenhouse. The results indicated lower levels of hydrogen peroxide and lipid peroxidation rate and increased activities of antioxidant enzymes and leaf chlorophyll content. Gusain et al. (2014) investigated the effect of T. harzianum and Fusarium pallidoroseum on biomass production, catalase, superoxide dismutase, and the peroxidase activities of rice under conditions of drought stress. The plants inoculated with plant growth-promoting fungi showed higher catalase, superoxide dismutase, and peroxidase activities as well as increased dry weight of the shoot and root. The study concluded that higher biomass as well as enhanced enzymatic activities may be the mechanism involved in the alleviation of drought stress and maintaining plant homeostasis under stress conditions. Gusain et al. (2015) reported drought stress amelioration in different cultivars of rice with the application of different PGPRs.

Guler et al. (2016) studied the effect of Trichoderma atroviride in maize seedlings under drought stress. The root colonization of fungus increased the fresh and dry weight of maize roots, prevented lipid peroxidation, and induced antioxidant enzyme activity while less hydrogen peroxide content was observed in response to drought stress in inoculated plants. Kanwal et al. (2017) concluded that PGPR in combination with compost and mineral fertilizer significantly reduced the effect of drought stress on wheat by positively influencing the physiological and biochemical parameters of wheat plants.

Ganjeali et al. (2018) conducted an experiment to examine the impacts of G. mosseae on improving the drought tolerance of the common bean. The inoculated plants showed increased dry weight of the root and shoot, phosphorus content, CO2 assimilation, relative water content, transpiration rate, superoxide dismutase, polyphenol oxidase and peroxidase activities, proline content, and leaf soluble proteins along with lower stomatal resistance as compared to the non-AM plants. Kour et al. (2019a) reported the alleviation of drought stress in wheat. Kour et al. (2020b) reported the mitigation of drought stress in the great millet with the inoculation of drought-adaptive, P-solubilizing S. laurentii. A study from Sood et al. (2020) reported the alleviation of drought stress in maize treated with B. subtilis. Kour et al. (2020c) showed the amelioration of drought stress in the fox tail millet treated with A. calcoaceticus and Penicillium sp. Thus, drought-adaptive microbes hold great potential for more sustainable agricultural activities and better food choices.

1.3.1.3: High temperature stress

Temperature is another major abiotic stress determining the growth and productivity of plants across the globe (Allakhverdiev et al., 2008; Archna et al., 2015; Zhu et al., 2011b). High-temperature stress causes a series of morphological, physiological, and biochemical changes in plants. Each species of plants has its own most favorable range of temperature for growth and reproduction. Therefore, extreme variations can exert a thermodynamic influence on nucleic acids and proteins as well as substructures of plant cells (Niu and Xiang, 2018; Ruelland and Zachowski, 2010; Verma et al., 2019). Plants have evolved diverse adaptation mechanisms for survival under such adverse conditions, among which the most common is the stress-induced gene expression activation of the adjustment of the plant metabolism (Iba, 2002). Thus, breeding efforts are also being focused on gene transformation to efficiently improve plant adaptability to extreme temperatures (Grover et al., 2000; Sharkey, 2000), but breeding techniques are not cost-effective and are time-consuming. Alternatively, there are reports of PGP microbes that could be used for inoculating crops under extremes of temperature so that the adverse effects of high temperature could be mitigated.

Zhu et al. (2011b) studied the effects of G. etunicatum symbiosis on gas exchange, chlorophyll fluorescence, and pigment concentration of maize plants under high-temperature stress. AM symbiosis improved the stomatal conductance and transpiration rate, chlorophyll content, carotenoids, water use efficiency, holding capacity of water, and relative water content. Wu (2011) evaluated the effects of G. mosseae on the growth, root morphology, superoxide dismutase and catalase activities, and soluble protein content of Poncirus trifoliata seedlings at low (15°C), optimum (25°C), and high (35°C) temperatures. Mycorrhizal colonization significantly increased superoxide dismutase (SOD) and catalase activities as well as soluble protein content at high temperature. The study suggested that the mycorrhizal alleviation of temperature stress in P. trifoliata seedlings was at high temperature while the alleviation was noticeably weakened at low temperature. The study from Sarkar et al. (2018) revealed that wheat inoculation with Ochrobactrum pseudogrignonense and B. safensis protected the plants from temperature stress.

1.3.1.4: Low temperature

Low-temperature stress is the most severe abiotic stress limiting crop growth and productivity worldwide (Bunn et al., 2009; Chen et al., 2013; Zhang et al., 2009). It could cause many injuries to plants including reduced cellular milieu osmotic potential, immediate mechanical constraints, macromolecule activity changes (Wu and Zou, 2010), increased accumulation of hydrogen peroxide (Zhang et al., 2009), and noteworthy alternation of the plasma membrane (Janicka-Russak et al., 2012). The use of PGP microbes has opened up new possibilities for the mitigation of chilling stress in plants (Verma et al., 2016, 2015; Yadav et al., 2019). Chen et al. (2013) revealed the potential of F. mosseae in the alleviation of low-temperature stress for cucumber seedlings. The inoculated seedlings had noteworthy higher fresh and dry weight; improved content of flavonoids, lignin, phenols, and phenolic compounds; and DPPH activity. Additionally, large increments have been observed in caffeic acid peroxidase, chlorogenic acid peroxidase, cinnamyl alcohol dehydrogenase, glucose-6-phosphate dehydrogenase, guaiacol peroxidase, phenylalanine ammonia-lyase, polyphenol oxidase, and shikimate dehydrogenase. Liu et al. (2017) studied the effect of G. mosseae on growth, antioxidant, osmoregulation, and nutrition in Vaccinium ashei and Vaccinium corymbosum plants exposed to low temperature. The study showed that inoculation with AM fungi enhanced ascorbate peroxidase, guaiacol peroxidase, glutathione, and superoxide dismutase activities in leaves while decreasing the concentrations of hydrogen peroxide, malondialdehyde, and superoxide anion radicals. Further, the inoculated plants had higher concentrations of soluble sugars and proline as well as phosphorus and potassium content.

In the study by Ghorbanpour et al. (2018), the effects of T. harzianum as a biocontrol agent were demonstrated on the tolerance of Solanum lycopersicum L. exposed to chilling stress. The study revealed that the strain mitigated the adverse effects of chilling stress. The study by Singh et al. (2020d) suggested that the coinoculation of Achromobacter xylosoxidans and T. harzianum could be a green initiative that could improve growth and mitigate cold stress in Ocimum sanctum. Thus, stress conditions greatly halt agricultural production. During stress conditions, plant growth is greatly affected. There could be nutritional and hormonal imbalances, increased susceptibility to disease, and much more. Plant growth could be increased by using microbial inoculants with PGP traits, which is in fact a novel as well as environmentally safe strategy.

1.3.2: Biotic stress management

Plant diseases act as biotic stress factors, causing farmers to suffer economic loss. Biotic stress also causes food spoilage during storage through toxin production. To combat these diseases, farmers rely on chemical fungicides and pesticides, which in turn are not safe for human health and the environment (Latha et al., 2019). Biotic stresses deprive their host of its nutrients and can lead to the death of plants (Gull et al., 2019). To get rid of such problems, the use of biocontrol agents for protecting plants from diseases has gained greater attention. The biocontrol agents utilizing PGP microbes appear to be an outstanding approach to maintain plant productivity and growth under biotic stress (Hashem et al., 2019). PGP microbes use a wide range of mechanisms to act as alleviators of biotic stress such as the production of antibiotics, hydrolytic enzymes, siderophores, HCN, and ammonia (Yadav et al., 2020b).

Antibiotics are low molecular weight organic compounds that play an active role in plant disease biocontrol and often act in concert with competition and parasitism (Jha, 2018). The important antibiotics known to play a major role in antibiosis include pyoluteorin, phenazines, and volatile HCN (Haas and Défago, 2005). Other identified antibiotics include 2,3-butanediol, 6-pentyl-α-pyrone, 2-hexyl-5- propyl resorcinol, and D-gluconic acid produced by endophytes (Dandurishvili et al., 2011). Pseudomonas strains are known to produce different types of antibiotics, including phenezine-1-carboxylate, pyoluteorin, and pyrolnitrin (Kour et al., 2019d; Kraus and Loper, 1995). Other antibiotics such as circulin, colistin, and polymyxin effective against Gram-positive and Gram-negative bacteria as well as phytopathogens have been reported from Bacillus sp. (Mahmood et al., 2019). The antibiotics fengycin, iturin, and surfactin have been reported from B. subtilis. Bacteriocins with a lower killing spectrum produced by bacteria have also played roles in the defense systems of plants against bacterial infection. Cell wall -egrading enzymes produced by bacteria can limit the activities of other microbes (Shoda, 2000). Chitinase and laminarinase producing P. stutzeri have been found to digest and lyse the mycelia of F. solani, preventing root rot (Lim et al., 1991).

β-1,3 glucanase producer Pseudomonas cepacia was shown to decrease the incidence of disease caused by Pythium ultimum, R. solani, and Sclerotium rolfsii by damaging the mycelia (Fridlender et al., 1993; Govindasamy et al., 2008). Siderophores are low molecular weight iron-chelating compounds with affinity for ferric ions; they are produced by microbes. There are different categories of siderophores with aerobactin, ferribactin, ferrioxamine, francobactin, and Schizokinen falling under the hydroxamate type whereas agrobactin, enterochelin, and parabactin are catecholates (Sayyed et al., 2013). Siderophores play a major role in biocontrol by binding most of the available Fe  + and preventing the growth of any pathogens. Some strains of Pseudomonas have been shown to suppress the activities of plant pathogens by producing siderophores or pseudobactin (Shoda, 2000). A study by Xia et al. (2020) reported the potential of Bacillus xiamenensis in suppressing the red rot of sugarcane and enhancing plant growth. Shahzad et al. (2021) reported the role of B. aryabhattai in protecting tomato plants from Fusarium wilt and plant growth promotion. PGP microbes as biocontrol agents are an efficient strategy against plant pathogens and in reducing the use of chemical agents.

1.4: Beneficial microbiomes for sustainable crop production and protection

Microbes, little wonders inhabiting diverse environmental conditions, are known to play various roles such as mineralization, biogeochemical cycles (phosphorus and nitrogen), and decomposition. These roles tend to maintain environmental cycles. Crop production is one such role that benefits the agriculturist to produce high-quality crops in a sustainable way. A beneficial microbial population or PGP microbes can improve crop production either by fulfilling nutrient requirements or by protecting the crop from pests and pathogens by inhibiting their growth (Yadav et al., 2018). PGP microbes can be used as biofertilizers and biopesticides for sustainable crop production, which can also help in achieving organic farming under normal and stress environmental conditions (Fig. 1.2).

Fig. 1.2

Fig. 1.2 Beneficial microbiomes with plant growth-promoting attributes as biofertilizers for PGP and soil fertility under natural and stressed conditions. Adapted with permission from Kour, D., Rana, K.L., Yadav, A.N., Yadav, N., Kumar, M., Kumar, V., et al., 2020d. Microbial biofertilizers: bioresources and eco-friendly technologies for agricultural and environmental sustainability. Biocatal. Agric. Biotechnol. 23, 101487. https://doi.org/10.1016/j.bcab.2019.101487.

1.4.1: Biofertilizers

Fertilizer is a basic need of the agricultural system. It is widely used in huge amounts all over the globe. It is mainly used for increasing crop productivity as necessary soil nutrients have been depleted drastically due to the overutilization of land resources and human activities. Currently, fertilizers used in agricultural fields are mostly chemically synthesized, which have various harmful aspects. The accumulation of harmful chemicals, pollution, and the loss of soil fertility as well as the biodiversity of animals, insects, and microbes are some negative effects of chemical-based fertilizers. Fertilizers will becomes an enemy of earth in sooner time. After years of studies, plant growth microbes have been recognized as a suitable product for agriculture (Singh et al., 2020a). Beneficial microbes in diverse habitats could be used as biofertilizers to fulfill required plant nutrients. They use different mechanisms through which they convert the insoluble form of nutrients to soluble forms of macro- and micronutrients by fixing, solubilizing, or chelating. The fixing mechanism is mainly used for availing nitrogen nutrients, which is known as biological nitrogen fixation. In this, atmospheric dinitrogen is fixed by microbes by secreting nitrogenase enzyme activity (Subrahmanyam et al., 2020).

Another microbe mechanism is solubilization, which can avail nutrients such as phosphorus, potassium, and zinc mainly by lowering the soil pH (Kaur et al., 2020a; Kour et al., 2020a). The lowering of pH is mainly achieved by the secretion of organic acids such as citric, gluconic, lactic, acetic, and oxalic acids (Kour et al., 2021b). Chelation is another microbial mechanism used to get iron from its ore. This mechanism usually fulfills the iron requirements of a plant. All these microbial mechanisms help in fertilizing crops and increasing the yield in a sustainable way (Rai et al., 2020). Much evidence has been published in reputed peer-reviewed journals. In a study, the rhizobacterium P. fluorescens was inoculated in wheat under a greenhouse. The inoculation resulted in enhanced grain yield and biomass (Smyth et al., 2011). In another investigation, the endophytic bacterium Bacillus sp. was reported to increase the leaf number, shoot length, and dry biomass of strawberries after inoculation (de Melo Pereira et al., 2012).

An actinomycetes identified as Streptomyces sp. was also recognized as a potent strain to be used in agriculture. Its use in inoculation has increased rice growth because it has the capability of secreting the most important class of phytohormones, that is, auxin (Gopalakrishnan et al., 2014). In a similar way, endophytes associated with sweet sorghum identified as Bacillus sp. and Pantoea sp. were reported as effective inoculum when tested on sorghum (Mareque et al., 2015). In another investigation, the IAA-producing bacterium Enterobacter sp. was reported as increasing wheat plant growth under salinity stress (Sorty et al., 2016). Rhizospheric microbes of Seabuckthorn and E. ludwigii were also reported as a potential microbial inoculum in stress regions, as it tested positive for solubilizing phosphorus (Dolkar et al., 2018). In another report, Acinetobacter guillouiae, an endophytic nitrogen fixing, K, Zn, P-solubilizing, IAA, ammonia producing bacteria was reported for enhancing the plant growth of wheat plants (Rana et al., 2020). The phosphorus-solubilizing bacterium Pseudomonas sp. was also reported as a PGPM when isolated from the high altitudes of Himalayan soil (Adhikari et al., 2021).

1.4.2: Biopesticides

Beneficial microbes also have been reported as efficient biocontrol agents. In agriculture, others inputs used in fields are pesticides, as various crops—mainly horticulture crops—are attacked by different pests and pathogens. These pests and pathogens tend to decrease crop productivity and sometimes complete erase the plant products. In order to prevent this, farmers use different types of biocontrol agents that are synthesized chemically such as fungicides, pesticides, and nematocides. These chemical products can adversely affect the health of the environment (Kour et al., 2021a). Pesticides have also been marked as dangerous pollutants of the Earth’s crust because they do not easily degrade and can remain on the Earth for a very long time. A main concern of environmentalists is also the bioremediation of such pesticides in soil for longer periods, as they also contribute to pollution and land degradation (Thakur et al., 2020).

The use of microbes as biocontrol agents is another remarkable facet of these little wonders that helps crop productivity in an ecofriendly way (Kumar et al., 2021a). Microbes exhibit different mechanisms for alleviating crop stress caused by pests and pathogens such as the production of ammonia, hydrogen cyanide (HCN), hydrolytic enzymes, and siderophores. Ammonia, HCN, and hydrolytic enzymes are used to kill microbes directly whereas siderophore production limits iron nutrients in the soil, killing pathogens because of nutrient deficiency (Yadav et al., 2020a). Different microbial species have been reported that have the potential to be biopesticides. In a study, Burkholderia pyrrocinia was reported for controlling the pathogens of poplar canker, that is, Cytospora chrysosperma, Fusicoccum aesculi, and Phomopsis macrospora, as they have the capability of producing different hydrolytic enzymes such as β-1, 3-glucanases, chitinases, and proteases (Ren et al., 2011). Another report found that Talaromyces flavus is a potential antagonistic against the causal agent of wilt disease (Naraghi et al., 2012). In another report, actinomycetes species identified as Streptomyces cyaneofuscatus, S. kanamyceticu, S. flavotricini and S. rochei were found to inhibit the growth of the cotton pathogen causing wilt, that is, Verticillium dahlia (Xue et al., 2013).

B. subtilis was also reported as a biocontrol agent that inhibits the growth of Fusarium sp. when tested in apple seedlings (Ju et al., 2014). In another report, P. aeruginosa was reported as a cogent strain that promotes plant growth and inhibits the growth of A. flavus and Fusarium oxysporum (Goswami et al., 2015). The fusarium wilt causing pathogen F. oxysporum also has been reported to be inhibited by the biocontrol agent identified as P. polymyxa (Du et al., 2017). In a similar report, Streptomyces sp. was also reported for inhibiting the causal agent of Fusarium wilt and the bacterial wilt of the tomato (Zheng et al., 2019). Another pathogenic species of genera Fusarium, that is, F. graminearum, a causal agent of corn stalk rot, was effectively inhibited by Bacillus velezensis (Wang et al., 2020). One of the most renowned biocontrol agent genera Trichoderma, that is, T. asperellum, was also reported to suppress the soilborne fungal phytopathogen F. oxysporum (Win et al., 2021).

1.5: Beneficial microbiomes in organic agriculture

Organic farming is a sustainable technique for the agro-ecosystem. This technique is used to enhance the Earth’s resources, genetic diversity, and crop production. Developing countries are bestowed with lot of potential to produce all varieties of organic products due to their various agro-climatic regions (Willer and Lernoud, 2019). Asia is endowed with various types of naturally available organic forms of nutrients in different parts of the continent, which will help in the organic cultivation of crops substantially. In India, only 40% of the cultivable area is affected by fertilizers where irrigation facilities are available and the remaining 60% of arable land is mainly rain-fed, so a negligible amount of fertilizers is used (Reganold and Wachter, 2016). Farmers in these areas often apply organic manure as a source of nutrients but microbes could also be utilized in organic farming to produce and protect plants and maintain soil health and fertility (Bhattacharjee and Dey, 2014).

1.6: Implication of beneficial microbes sustainable economic

The production of biofertilizers is always demand-driven; demand creation among farmers is the most important step toward biofertilizer promotion (Mazid and Khan, 2015). The commercial biofertilizer history began in 1895 with the launch of nitragin, a rhizobia culture. About 170 organizations in 24 countries are involved in the commercial production of biofertilizers. In India, the first commercial production started in 1956 at the Indian Agricultural Research Institute, New Delhi, and the Agricultural College and Research Institute, Coimbatore. The Ministry of Agriculture under the 9th plan put effort in promoting and popularizing the input by setting up the National Project on Development and Use of Biofertilizers (Ghosh, 2004). The commonly used biofertilizers in India include Azospirillum, Azotobacter, blue green algae, Rhizobium, and phosphate solubilizing and mobilizing biofertilizers. The current global market for agricultural products raised through organic farming is valued at around $30 billion with a growth rate of around 8% (Mishra and Dash, 2014). The government of India and the different state governments have been promoting biofertilizers through extensions, grants, and subsidies on sales with varying degrees of emphasis. Farmers are also learning about the technology. The enterprise of firms operating through their marketing, research, and development efforts will lead to the widespread use of resources as soon