Rhizosphere Engineering

By PANKAJ KUMAR

Rhizosphere Engineering is a guide to applying environmentally sound agronomic practices to improve crop yield while also protecting soil resources. Focusing on the potential and positive impacts of appropriate practices, the book includes the use of beneficial microbes, nanotechnology and metagenomics. Developing and applying techniques that not only enhance yield, but also restore the quality of soil and water using beneficial microbes such as Bacillus, Pseudomonas, vesicular-arbuscular mycorrhiza (VAM) fungi and others are covered, along with new information on utilizing nanotechnology, quorum sensing and other technologies to further advance the science.

Designed to fill the gap between research and application, this book is written for advanced students, researchers and those seeking real-world insights for improving agricultural production.

• Explores the potential benefits of optimized rhizosphere
• Includes metagenomics and their emerging importance
• Presents insights into the use of biosurfactants

• Language: English
• Publisher: Academic Press
• Release date: Feb 15, 2022
• ISBN: 9780323885959

Book preview

Chapter 1: Plant growth promotion by rhizosphere dwelling microbes

Elizabeth Lewis Roberts    Southern Connecticut State University, New Haven, CT, United States

Abstract

This work summarizes the roles of various plant promoting (PGP) microorganism on several types of plant hosts. In particular, rhizosphere dwelling bacteria and fungi that increase plant growth, protect plants from pathogens, and increase tolerance to abiotic stresses are presented. These traits are due, in part, to the production of enzymes, hormones, and a plethora a various metabolites produced by rhizosphere microorganisms that directly or indirectly benefit the plants. The impact of selective grazing by bacterivorous protozoa on plant growth promotion is also examined. In addition to reviewing research from other investigators, this paper introduces a recently isolated Pseudomonad bacterium that has demonstrated growth promotion and protection of heirloom tomato (Solanum lycopersicum) in the face of both abiotic and biotic stresses. Our findings indicate that the novel Pseudomonas koreensis strain could serve as an agricultural inoculant to induce plant growth and protection. The potential to create effective bioinoculum using rhizosphere microorganisms is discussed.

Keywords

Plant growth promoting Rhizobacteria; Plant growth promoting fungi; Bacillus; Pseudomonas; Trichoderma; Protozoa

Chapter outline

1.1Introduction

1.2Plant growth promoting rhizobacteria (PGPR)

1.2.1Pseudomonads

1.2.2Bacillus and paenibacillus

1.2.3Streptomyces

1.3Plant growth-promoting fungi (PGPF)

1.3.1Piriformospora

1.3.2Trichoderma

1.3.3Fusarium

1.3.4Penicillium

1.4Plant growth-promoting protozoa

1.5Conclusions

References

1.1: Introduction

The phyllosphere and rhizosphere serve as breeding ground for every type of microorganism. While many of the microbes associated with plants can be harmful inhabitants, there are examples across the board of beneficial bacteria, fungi, and protozoa. These microbial colonizers promote plant health and growth either directly or indirectly. Whatever the effect, the benefits depend both on the type of microbe and the variety of plant.

The beneficial bacteria are known as PGPB (plant growth-promoting bacteria) and PGPR (plant growth-promoting rhizobacteria) when they are rhizosphere dwellers. Plant growth-promoting bacteria are known to inhabit the rhizosphere due to the presence of specific exudates, which are believed to be the underlying reason that different plants harbor different microbial colonizers (Haichar et al., 2008). PGPB and PGPR directly promote growth with nitrogen fixation, the production of organic acids, siderophores, and various phytohormones. Nitrogen and phosphorus are growth limiting factors for plants (White et al., 2015). Phosphorus plays a role in several biological steps but is highly unavailable for plant growth. Phosphate solubilizing bacteria derive insoluble and inorganic phosphate and make it available to plants via mineral phosphate solubilization (Hayat, Ahmed, & Sheirdil, 2012). Nitrogen acquisition is required for the production of proteins and nucleic acids. Without an adequate nitrogen supply, plants fail to develop properly (White et al., 2015). Siderophores are low molecular weight compounds chelate iron, ultimately making it unavailable to pathogens (Kumar, Menon, Agarwal, & Gopalakrishnan, 2017). Therefore, siderophore production is typically associated with plant protection. However, there is also indication that microbial siderophores can donate iron to plants through iron-regulated outer membrane proteins (IROMP) (Sayyed, Chincholkar, Reddy, Gangurde, & Patel, 2013). As this element is essential to metabolic processes and, thus, plant growth, siderophore producing microbes could be important components to plants in iron deficient soils. Similarly, the phytohormone indole-3-acetic acid (IAA) is responsible for the regulation of root and shoot growth, especially in response to light and gravity. While IAA is not needed for bacterial growth, it is produced by many plant-associated bacteria. In fact, IAA is produced by 80% of rhizobacteria, which are generally regarded as plant mutualists. Finally, PGPR can directly promote plant health through mechanisms such as suppressing ethylene production due to stress with ACC deaminase.

Indirectly, PGPR increase plant health by preventing the growth of phytopathogens that cause plant diseases. PGPR negatively impact plant pathogens through a number of different modes, including competing for space and nutrients, production of hydrolytic enzymes, and inhibition of toxins. Importantly, these organisms can play a role in induced systemic resistance against pathogens and/or increased abiotic stress tolerance.

While much is known about PGPR, fewer studies highlight the benefits of colonization by nonpathogenic fungal rhizosphere inhabitants. Also known as plant growth-promoting fungi (PGPF), these fungi can decrease the severity of abiotic stresses such as drought, UV radiation, or high salt, which can damage plants and decrease their productivity. PGPF also protects plants through niche exclusion, antibiosis, production of lytic enzymes, and hyperparasitism (Hyakumachi, 1994; Naziya, Murali, & Amruthesh, 2020). For instance, PGPF produced enzymes chitinases and glucanases defend plants from fungal pathogens while inducing resistance in hosts (Naziya et al., 2020). These fungi also mobilize vital nutrients such as phosphorus and iron, making them more available to host plants. While less is known about plant growth-promoting fungi, there is a plethora of research on the benefits of mycorrhizal colonization. As such, mycorrhizal inoculants are widely used as commercial additives to improve plant growth. While nutrient exchange and thus potential benefit to fungal mutualists is clearly documented in mycorrhiza, the mechanisms are still to be fully determined in other beneficial interactions between plants and fungi.

Rhizosphere protozoa can also benefit plants growing in their vicinity. Amoeba, flagellates, and ciliates can make up as much as several million cells per gram of rhizosphere soil (Ekelund & Rønn, 1994). In many of the studies documenting plant growth promotion by rhizosphere protists, selective grazing is referenced. Flagellates and ciliates are limited to preying upon bacteria of a certain size, predominantly feeding upon medium sized bacterial cells. Moreover, certain bacteria emit chemicals that inhibit bacterivorous protists. Each of these can lead to protozoan regulation of both the size and taxonomic composition of rhizosphere bacterial communities (Simek et al., 1997).

1.2: Plant growth promoting rhizobacteria (PGPR)

Interactions between plant growth-promoting rhizobacteria and adjacent plants lead to increased seedling emergence, increased biomass, increased mineral and water uptake, and overall increased plant vigor (Hayat et al., 2012). To reiterate, the exact results are dependent on plant and microbe types. Some bacteria make N2 and phosphates available, while others produce antimicrobial substances that ward of phytopathogens. Additionally, some rhizosphere dwelling bacteria promote plant growth through the production of plant hormones such as IAA, cytokinin, and gibberellic acid. Finally, PGPR helps stave of abiotic stresses through the production of vitamins such as thiamine, niacin, riboflavin, biotin, and pantothenic acids (Hayat et al., 2012).

Additionally, plants that grow in the vicinity of PGP bacteria are defended from phytopathogens through antibiotics and antifungal compounds. These compounds play a dual role as they are likely also responsible for intraspecific competition and self-defense of their producers. Antifungal enzymes produced by PGPR include chitinases and β-1,3 glucanases that break structural integrity of fungal cell walls. PGPR also produce siderophores and antibiotics, which limit the growth of bacterial phytopathogens.

1.2.1: Pseudomonads

Pseudomonads are diverse in their ecology with both plant growth-promoting (PGP) and plant pathogenic strains. As colonizers of many types of plants, these bacteria survive partly through their production of lytic enzymes, antimicrobials, and volatile compounds. Plants associated with PGP pseudomonad strains benefit from bacterial produced chemicals that enhance plant growth or protect against plant pathogens (Compant, Duffy, Nowak, Clement, & Barka, 2005). The plant growth-promoting traits determined for Pseudomonas sp. include the production of siderophores, indole-3-acetic acid (IAA), phosphate solubilization, and nitrogen fixation. Pseudomonas sp. also make organic acids such as gluconic, citric, succinic, and α-ketobutyric acid, which benefit plants growing in their vicinity (Pal, Tilak, Saxena, Dey, & Singh, 2001). Moreover, rhizosphere dwelling pseudomonads produce well-characterized antibiotics such as 2,4-diacetylphloroglucinol, phenazine, pyroolnitrin, and pyoluteorin (Haas & Defago, 2005). Similarly, many pseudomonads produce endochitinases and chitobiosidases, which degrade cells of fungal pathogens (Nielsen & Sorensen, 1999). Additionally, PGP pseudomonads have been linked to induced systemic resistance in their plant hosts.

A multitude of studies focus on the abiotic stress tolerance provided to plants by inoculation of the rhizobacteria Pseudomonas sp. (Vyas, Rahi, & Gulati, 2009). Some strains of Pseudomonas help host plants tolerate drought. PGP pseudomonads seem to have a higher efficiency rate in environments that are drought prone, which is linked to their production of 1-aminocyclopropane-1-carboxylate also known as (ACC)-deaminase (Arshad, Shahroona, & Mahmood, 2008). ACC deaminase producers act as a sink in the rhizosphere by removing endogenous ethylene from the soil (Arshad et al., 2008). This protects nearby plants from excess ethylene, which typically results in decreased leaf growth.

Consequently, pseudomonads are commonly sought after as biological control strains due, in part, to the antimicrobial chemicals they produce. The bacterial root rot pathogens Pectobacterium and Dickeya spp. are both eliminated by the inoculation of Pseudomonas sp. (Sachdev & Cameotra, 2013). A study performed by Pal and colleagues highlighted that in the presence of Pseudomonas cepacea, there is an 80% reduction in infection from several Fusarium pathogens (Pal et al., 2001). Fusarium strains induce symptoms such as wilting, root rot, bulb rot, and head blight in several plant species. These PGP pseudomonads that protect against these fungi produce the antifungal compounds cyanide and florescent pigments (Pal et al., 2001). Likewise, the chemical 2,4-diacetylphloroglucinol (DAPG) has been indicated as a primary compound responsible for the biological control activity in fluorescent pseudomonads. With DAPG, these bacteria control the growth of pathogenic bacteria, fungi, and nematodes (Bergsma-Vlami, Prins, & Raaijmakers, 2005). DAPG producing Pseudomonas fluorescens strains have been noted in control of take-all-patch of wheat caused by Gaeumannomyces graminis var. tritici (Bergsma-Vlami et al., 2005). Additional antimicrobial chemicals produced by PGP pseudomonads are the siderophores. Sayyed et al. (2013) reported siderophore protection of potato from Erwinia carotovora by P. fluorescens and P. putida as well as protection of wheat from G. graminis by P. florescens and P. aureofaciens. Siderophores have also been linked to control of Fusarium oxysporum infection in onions by P. cepacia (Sayyed et al., 2013).

In addition to antimicrobial compounds, pseudomonads can also use quorum quenching to control growth of bacterial pathogens. Quorum quenching is a process by which the quorum sensing molecules that allow bacteria to sense their population size and coordinate responses such as expression of virulence factors that aid in their entry into susceptible plants are destroyed or modified. Quorum quenching interrupts the quorum sensing process through mechanisms such as breaking down the quorum sensing molecules such as acyl-homoserine lactone (AHL). Rodríguez et al. (2020) found that Pseudomonas segatis, P6, naturally displayed quorum quenching through enzymatic degradation of AHLs resulting in the reduction of infection by the bacterial phytopathogens Dickeya solani, Pectobacterium atrosepticum, and Pectobacterium carotovorum sp. carotovorum.

Several plant-associated pseudomonads inhibit infection by microbial pathogens through the production of cyclic cationic lipopeptides, such as polymyxin, and cyclic noncationic lipopeptide, such as the fusaricidins, which are active against both bacteria and fungi (Grady, MacDonald, Liu, Richman, & Yuan, 2016). Fluorescent pseudomonads, in particular, have been shown to produce cyclic lipopeptide (CLP) biosurfactants (Kruijt, Tran, & Raajimakers, 2009; Raaijmakers, de Bruijn, & de Kock, 2006). These secondary metabolites are essential for controlling mobility of producers through the reduction of surface tension and required for many of these bacteria to colonize plant microbial disease agents (Toribio et al., 2011). An interesting aspect of biosurfactants is that they can alter bioavailability, which can impact the presence of siderophores and cell wall degrading enzymes (D’aes, Maeyer, Pauwelyn, & Hofte, 2010). Therefore, it is not surprising that biosurfactants have also been linked to control the growth of plant pathogens including oömycetes, fungi, and bacteria (Geudens & Martins, 2018; Hultberg, Alsberg, Khalil, & Alsanius, 2010). Furthermore, many cyclic lipopeptide biosurfactant producing bacteria are recognized by the United States Environmental Protection Agency for biological control of plant diseases (Geudens & Martins, 2018). The use of biosurfactants as agrochemical solutions has grown exponentially as they are renewal resources with little to no toxicity (Kosaric & Sukan, 2015; Sachdev & Cameotra, 2013). Thus, pseudomonads bacteria are of interest for use in sustainable agriculture (Raaijmakers et al., 2006).

A fluorescent pseudomonad was isolated from the rhizosphere of a Japanese Maple (Acer palmatum) in Connecticut, USA. 16S rRNA gene sequences and phylogenetic analysis were performed to identify the isolate, which was identified as Pseudomonas koreensis JDSCSU15. P. koreensis strains have been identified from locations around the world (Hultberg, Alsberg, et al., 2010; Lozano, Bravo, & Handelsman, 2017) but were first isolated from sites in Korea and Mexico (Kwon et al., 2003; Toribio et al., 2011). The Mexican and Korean strains are phenotypically similar except in the ability to produce CLPs, which is exclusive to the Mexican strains (Toribio et al., 2011). The Connecticut strain also produces a biosurfactant (Fig. 1.1).

Fig. 1.1

Fig. 1.1 Halos of atomized mineral oil droplets modified by the biosurfactant produced by Pseudomonas koreensis JDSCSU15 grown overnight on Tryptic Soy agar medium.

The application of the biosurfactant has demonstrated plant growth promotion and protection in tomato. Furthermore, the biosurfactant reduces the growth of the tomato pathogen Xanthomonas campestris pv. campestris, which causes bacterial leaf spot disease, makes ACC deaminase, and solubilizes phosphates. Hultberg, Alsberg, et al. (2010) and Hultberg, Bengtsson, and Liljeroth (2010) studied a strain of P. koreensis that was found to protect plant hosts from biotic stresses. P. koreensis strain 2.74 produces a CLP with a molecular mass identical to the biosurfactant lokisin that suppresses disease in tomato caused by Pythium ultimum and in potato by Phytophthora infestans. Likewise, biosurfactants are gaining popularity over synthetic surfactants in agriculture to decrease phytopathogens, as well as in the application of pesticides (Khire, 2010; Sachdev & Cameotra, 2013). Therefore, the antimicrobial compounds present in the P. koreensis JDSCSU15 biosurfactant make it a particularly interesting prospect for controlling plant pathogens.

Heirloom tomato plants inoculated with P. koreensis JDSCSU15 displayed fewer drought symptoms than noninoculated controls after being deprived of water (Fig. 1.2). Drought stress severity (DSS) of inoculated and noninoculated plants were also compared for the four heirloom tomato varieties. Inoculated plants from each variety had fewer than 40% drought stress symptoms compared with 100% symptoms exhibited by control plants with Big Rainbow and Brandywine varieties displaying fewer than 20% symptoms (Fig. 1.2E). Inoculation of the bacteria to Big Rainbow variety of heirloom tomato also resulted in increased stem height over noninoculated controls when grown at higher than optimal temperatures (Fig. 1.3).

Fig. 1.2

Fig. 1.2 Noninoculated control plants from heirloom tomato varieties Big Rainbow (A), Brandywine (B), Burpee C (C), and Sweet Baby girl (D) subjected to drought conditions displayed classic drought symptoms such as wilting whereas plants inoculated with P. koreensis JDSCSU15 showed fewer symptoms. Drought stress ratings (E) were calculated by counting the number of wilted leaves per pot.

Fig. 1.3

Fig. 1.3 Under optimal temperature (25 °C), inoculation with Pseudomonas koreensis JDSCSU15 did not impact plant growth, whereas, at increased temperature (32 °C), the P. koreensis inoculated plants displayed greater height than noninoculated plants.

Heirloom tomato plants inoculated with P. koreensis JDSCSU15 isolate appeared to grow normally, with identical physical characteristics to the noninoculated controls. However, under heat stress, the P. koreensis inoculated plants were less impacted than controls (Fig. 1.3).

These results suggest that P. koreensis inoculation increases abiotic stress tolerance in tomato. While it is currently unknown what occurs during P. koreensis colonization that increases stress tolerance, it could result from the production of plant growth-promoting compounds such as ACC (1-aminocylopropane- 1-carboxylate) deaminase. ACC deaminase reduces ethylene levels, causing increased root length, which could allow the plant to access additional pockets of water, which would be beneficial in times with increased water loss through transpiration that would occur during higher temperatures (Shaikh, Sayyed, & Reddy, 2016). Observed increases in shoot and roots were likely results of indole-3-acetic acid, which is produced by the P. koreensis strain. Inoculation with P. koreensis JDSCSU15 also helps to reduce the symptoms of pathogenesis by Fusarium oxysporum fsp. Lycopersici. Our experiments showed that when the P. koreensis strain was added to tomato rhizospheres prior to infection with the fungus, plants had higher dry weights than noninoculated controls (Fig. 1.4). Importantly, the P. koreensis JDSU15 inoculated plants also had significantly greater dry weights over noninoculated controls (p = 0.008).

Fig. 1.4

Fig. 1.4 Tomato plants inoculated with P. koreensis JDSCSU15 showed greater growth than noninoculated plants even in when plants were infected with tomato wilt pathogen, Fusarium oxysporum fsp. Lycopersici ( p  = 0.008).

Heirloom tomatoes infected with the bacterial pathogen Xanthomonas campestris and treated with P. koreensis JDSCSU15 bacteria or the P. koreensis biosurfactant were significantly larger than those that were untreated. Several virulent strains of the bacterium X. campestris pv. vesicatoria cause leaf spot on tomatoes. The height of plants infected by X. campestris and treated with biosurfactant showed impressive growth when compared to those without treatment. The average height of the control group (22.2 cm ± 1.13) was taller than the average height of infected tomatoes that were untreated (16.34 cm ± 0.55), while the average height of infected tomatoes treated with P. koreensis (22.0 cm ± 1.35) was shorter when compared with the average height of the infected tomatoes treated with P. koreensis biosurfactant (29.71 cm ± 0.82). The tomatoes infected with X. campestris and treated with P. koreensis biosurfactant were significantly taller than the control group (p = 0.04) as well as the group that was infected and untreated (p = 0.006) (Fig. 1.5).

Fig. 1.5

Fig. 1.5 Heirloom tomatoes, infected with Xanthomonas campestris and treated with P. koreensis JDSCSU15 inoculum or purified biosurfactant. The average height of the plants infected with X. campestris and treated with P. koreensis biosurfactant was significantly higher than the control group ( p  = 0.043466353) and the tomatoes infected with X. campestris and untreated ( p  = 0.006949734).

Since P. koreensis JDSCSU15 enhanced tolerance of tomato to drought and heat stress, it could be a helpful soil inoculum. In addition, plate assays indicated siderophore production and phosphate solubilization while IAA production was determined by comparing absorbance of P. koreensis supernatant in Salkowski reagent with a standard IAA (data not shown). With these findings, we may be on the brink of using the novel P. koreensis as a phytostimulant and as biological control against biotic and abiotic stressors.

Moreover, the P. koreensis biosurfactant showed significant protection to tomato against pathogenic X. campestris. In agriculture, biosurfactants are gaining popularity over the synthetic surfactants to decrease phytopathogens and as aids in the application of pesticides (Sachdev & Cameotra, 2013). Additionally, biosurfactants are renewable resources, with high specificity, high surface activity, and great resilience under harsh conditions (Sachdev & Cameotra, 2013). Therefore, the antimicrobial compounds present in the P. koreensis JDSCSU15 biosurfactant make it a particularly interesting prospect for use in agriculture.

1.2.2: Bacillus and Paenibacillus

Bacilli are well known for their PGP traits and impact plants through direct and indirect mechanisms. Plant growth-promoting bacilli produce auxin, siderophores, ammonium, and proteases and are known for inorganic phosphate solubilization (Hayat et al., 2012; Kumar et al., 2020). As with the Pseudomonads, production of siderophores, hydrolytic, enzymes, and antibiotics by Bacillus strains can directly or indirectly protect plants from microbial pathogens. Nitrogen fixation is a direct mechanism of plant growth promotion that can be documented through the presence of nitrogenase (nif) genes. The nif genes have been found in B. safencis, B. licheniformis, B. cereus, B. megaterium, B. aerophilus, B. flexus, and B. subtilis. B. aryabhattai SRB02 produces the plant hormones IAA, cytokinnin, gibberellic acid, and abscisic acid (Park et al., 2017). High levels of abscisic acid are thought to be responsible for the increased heat stress tolerance demonstrated in soybean plants treated with SRB02 strain over the untreated plants (Park et al., 2017).

In the cereals, rice, and switchgrass, strains of Paenibacillus have been shown to influence plant growth through IAA production, nitrogen fixation, and phosphate solubilization (Padda, Puri, Zeng, Chanway, & Wu, 2017). Previously categorized in the genus Bacillus, Paenibacillus strains have also produce chitinases, which decrease infection by fungal phytopathogens (Kumar et al., 2012). An additional rice rhizosphere isolate, Bacillus amyloliquefaciens, has been shown to produce IAA and ACC deaminases (Nautiyal et al., 2013). In general, the rhizospheres of grasses are dominated by these plant growth-promoting bacteria. Interestingly, many of these bacteria are vertically transmitted (Roberts & Adamcheck, 2017). Studies on vertical transmission in other plants could provide a better understanding of the relationships between plant growth-promoting rhizosphere dwelling Paenibacillus strains and grass plants.

1.2.3: Streptomyces

The Streptomyces are well-documented plant growth promoters. They secrete vitamins and enzymes and produce indole-3-acetic acid, which would each help to increase plant growth (Myo et al., 2019). In fact, Streptomyces species have been found to be the dominant IAA rhizosphere producing actinobacterial strain (Myo et al., 2019). Specifically, Streptomyces roseoflavus NKZ-259 has demonstrated antifungal activity toward the pathogens Botrytis cinerea, Curvularia lunata, Alternaria alternate, Colletotrichum gloeosporioides, Rhizoctonia cerealis, and Ustilaginoidea virens (Shi et al., 2018). Streptomyces fradiae NKZ-259 application to tomato seedlings resulted in a twofold increase in growth over noninoculated controls (Myo et al., 2019). Liu et al. (2019) found that Streptomyces sp. NEAU-S7GS2 controls mycelial growth and sclerotia germination in the fungal pathogen Sclerotinia sclerotiorum, which causes stem rot in many economically important crops. The strain NEAU-S7GS2, which was isolated from the rhizosphere of Glycine max, produces ACC deaminase, IAA, and solubilizes phosphates. Liu et al. (2019) also found that this strain synthesizes siderophores. With these examples, it is clear why Streptomyces actinobacteria are sought after for use as biofertilizers.

1.3: Plant growth-promoting fungi (PGPF)

Similar to PGPR, the plant growth-promoting fungi help host plants with increased growth but also tolerance to biotic and abiotic stresses. As many rhizosphere-associated fungi are phytopathogens, the majority of research regarding plant growth-promoting fungi is on mutualistic endophytes such as in the Clavicipitaceae or on mycorrhizae (Murphy, Doohan, & Hodkinson, 2015; Roberts & Lindow, 2014). For example, endophytic fungal colonizers of grasses were shown to increase the presence of plant growth-promoting in the rhizosphere of host plants (Roberts & Ferraro, 2015; Roberts & Lindow, 2014). PGPF are known to produce enzymes such as PAL (phenylalanine-lyase), POX (peroxidases), chitinases, and β-1,3-glucanases, all of which can accumulate in host plants and defend against fungal phytopathogens. PGPF are known to protect plants from phytopathogen infection through niche exclusion, antibiosis, production of lytic enzymes, and hyperparasitism (Jogaiah, Abdelrahman, Tran, & Shin-ichi, 2013; Naziya et al., 2020). Plant protection by fungi has also been linked to siderophore production (Murphy et al., 2015).

1.3.1: Piriformospora

Piriformospora indica are biotrophic fungal mutualists that can colonize roots of many types of plants. Thus, P. indica strains are often used as bioinoculum to aid in plant growth (Gill et al., 2016). It has a high affinity phosphate transporter (PiPT) (Yadav et al., 2010). Yadav et al. (2010) found that P. indica has a high affinity phosphate transporter. The PiPT increases phosphate, which has been shown to increase biomass in Zea mays colonized by P. indica. However, some reports on this transporter indicate that it does not always favor the plant. Apparently, positive results are host dependent as the PiPT showed no increased biomass in Nicotiana attenuata (Barazani, Benderoth, Groten, Kuhlemeier, & Baldwin, 2005).

In Arabidopsis, P. indica provides increased drought tolerance (Gill et al., 2016). In wheat, the fungus can increase tolerance to salinity. The abiotic stress response genes DRRB2A, ANAC072, CBL1, and RD29A are thought to be responsible for these actions. Additionally, the fungus employs the osmoprotectants betain, proline, and glycine. P. indica infection is also linked to induced systemic resistance to pathogenic fungi. Activation of pathogenesis-related (PR) proteins as well as upregulation of ERF1, which is responsible for ethylene production and LOX2 (jasmonic acid), are responsible for this resistance.

1.3.2: Trichoderma

Species of Trichoderma are well documented for their biological control properties. These fungi are mycoparasites, antibiotic producers, and, in fact, these rhizosphere dwellers are ingredients of several commercially available plant pathogen controls. Moreover, several species serve as commercially available biological fungicides. They are also known to control the insects. Zhang et al. (2017) showed that wheat seedlings coated with Trichoderma longibrachiatum TL6 conidia are protected from Heterodera avenae nematode. This makes sense as TL6 has a direct parasitic effect on both eggs and early juveniles of this economically important nematode. While nematicides offer good control in, some are associated with pollution of groundwater and soils while others can lower populations of beneficial soil microbes. TL6 suspensions could be an environmentally friendly alternative to nematicides (Zhang, Gan, & Xu, 2016). Other Trichoderma strains have demonstrated PGP properties in Arabidopsis thaliana. T. viridae application increases growth of the model organism (Hung, Lee, & Bennett, 2013), and T. asperellum ISM T5 decreases symptoms associated with Botrytis cinerea and Alternaria brassiociola infection through the production of the volatile compound 6-pentyl-α-pyrone (6PP). The volatile produced by ISM T5 increases expression in plant defense-related genes, which results in increased resistance to future pathogen infections (Kottb, Gigolashvili, Grobkinsky, & Piechulla, 2015). Another example of antifungal properties by Trichoderma was illustrated in a paper by Naziya et al. (2020), which showed that rhizosphere dwelling Trichoderma sp. NBP-66 and NBP-67 had 79.81% and 82.33% antagonism toward pathogenic Colletotrichum capsici on chili plants. Importantly, the Trichoderma strains were able to colonize the root without displaying pathogenicity toward the host plants. Another study on Trichoderma indicated that these fungi can recognize volatile compounds emitted from pathogenic Fusarium oxysporum and respond by increased expression of biological control genes that result in inhibition of the pathogen (Li et al., 2018).

1.3.3: Fusarium

The Fusarium species are ubiquitous in soil and are commonly known as plant pathogens. However, some strains have demonstrated plant growth promotion traits. A variety of Fusarium strains were shown to augment growth in Arabidopsis thaliana and Nicotiana tabacum through the production of volatile organic compounds (Bitas et al., 2015). Their research showed that the volatile organic compounds (VOCs) produced by this fungus promote shoot and root growth through an auxin-dependent mechanism. VOCs from F. oxysporum strains NRRL26379 and NRRL38335 increased chlorophyll content and lateral root development over noninoculated A. thaliana plants (Li & Kang, 2018). Furthermore, VOC treated A. thaliana plants infected with phytopathogenic Pseudmonas syringae had fewer symptoms than untreated controls (Li & Kang, 2018).

Naziya et al. (2020) found that Fusarium sp. NBP-65 isolated from chili rhizospheres had lower protection of the plant roots from Colletotricum sp. when compared to other Fusarium isolates. Moreover, NBP-65 was often not able to colonize the roots of the chili plants and when it did caused necrosis. Therefore, while there can be some protection to plants from Fusarium, it may not be a good choice in all plant hosts. In fact, whether F. oxysporum is pathogenic, asymptomatic, or beneficial to hosts can be determined by plant hormones and is thus dependent on host phenotype (Di, Takken, & Tintor, 2016).

1.3.4: Penicillium

Species of genus Penicillium are well known for the production of secondary metabolites such as phytohormones or amino acids, both of which stimulate growth in plants. A study on sesame showed that plants inoculated with Penicillium sp. NICS01 and Penicillium sp. DFC01 had increased shoot length, longer roots, and enhanced dry weights over noninoculated controls (Radhakrishnan, Kang, Baek, & Lee, 2014). This growth was attributed to the ability of these Penicillium strains to secrete amino acids, which helped the plants. Furthermore, both fungi protected the sesame from the stress of high salinity in soil and from pathogenesis from Fusarium spp. (Radhakrishnan et al., 2014). A study on tomato showed that Penicillium sp. EU0012 significantly reduced wilt symptoms caused by F. oxysporum f. sp. lycopersici (Alam, Sakamoto, & Inubushi, 2011). Penicillium strains are also known to make siderophores, which sequester iron from rhizosphere soils protecting plants from microbial pathogens.

1.4: Plant growth-promoting protozoa

Interestingly, the presence of some protozoa has been shown to positively impact plant health. Rhizosphere dwelling protists can directly influence plant health by preying on plant pathogens. Conversely, protozoa can indirectly promote plant growth by shaping the microbial community structure toward an abundance of plant growth promoting microorganism. Protozoa can stimulate production of antibiotics and siderophores as well as promote production of plant growth hormones. In particular, plant growth-promoting rhizobacteria have been shown to upregulate production of secondary metabolites in the presence of protozoa. Coinoculation of Acanthamoeba castellanii with a variety of plant growth-promoting Pseudomonas strains inhibited pathogenic infection of Pythium ultimum on wheat (Triticum aestivum). Furthermore, coinoculation of protozoa correlated with increased shoot fresh weight during Pythium infection. The bacteria responded to the presence of protozoan coinoculum by upregulating 2,4-DAPG or cyclic lipopeptides. This information is important as application of PGP bacteria may be more successful with coinoculation of certain protozoa (Weidner, Latz, Agaras, Valverde, & Jousset, 2017). On a similar note, Kuppardt, Fester, Härtig, and Chatzinotas (2018) found that the concentration of plant stress chemicals such as polyols decreased in maize inoculated with particular protists. Their analysis surmised that the difference in stress chemicals was due to shifts in rhizosphere bacterial community, which resulted from selective grazing. Xiong et al. (2020) found that phagotrophic protozoans enhance pathogen-suppressing genes in rhizosphere bacteria and that the community structure of phagotrophic protozoa at the time plants are established is an indicator of later plant health. Several researchers have demonstrated that protozoan grazing influences the bacterial community structure (Rønn et al., 2002; Rosenberg et al., 2009).

Protozoa influence microbial community composition. When compared to other rhizosphere fauna (nematodes and earthworms), protozoa had the largest impact on selective grazing, which was concluded to be due to the increase in plant growth promoting rhizosphere bacteria (Bonkowski & Brandt, 2002; Rosenberg et al., 2009). Protozoa were also found to increase the biomass of nitrifying bacteria following chloroform fumigation in experimental chambers planted with the grass Hordelymus europeaus (Alphei, Bonkowski, & Scheu, 1996). Similarly, plant growth was higher in experimental chambers that had protozoa than in those that had nematodes (Alphei et al., 1996). This could be due, in part, to the bacterivorous protozoa releasing bound nitrogen from bacterial biomass and delivering it back into the food web. As bacteria have more nitrogen than protozoa require, excess N available as ammonium is released and available for nearby plants to absorb, which could increase biomass.

While protozoan–bacterial relationships seem to benefit from increased plant root exudation, it seems the presence of ectomycorrhizal fungi changes everything. In pot experiments, mycorrhizal and nonmycorrhizal Norway Spruce (Picea abies), which were inoculated with either bacteria suspensions or bacteria plus protozoa suspensions, showed increased root length and branching with the addition of protozoa and no mycorrhizae (Bonkowski, Jentschke, & Scheu, 2001). Rønn, McCaig, Griffiths, and Prosser (2002) found that there were significantly more protozoa present when mycorrhizae were absent in Pisum sativum after 3 weeks in pot experiments. Conversely, when the fungi were absent, protozoa and bacterial populations increased. Mycorrhizal fungi are typically a carbon sink. As such, these fungi might impact root exudates, resulting in decreased nutrient availability for other PGP microbe populations. Therefore, while mycorrhizae are beneficial to plants, in general, they could influence the population size of other PGP microbes.

1.5: Conclusions

The rhizosphere supports a diverse set of microorganisms as it contains high nutrient value due to the abundance of root exudates and mucilages. In fact, PGPR are drawn to certain rhizospheres due to the presence of specific exudates. Soilborne plant growth promoting fungi may also be attracted to certain plants, but likely survive of a combination of decayed plant and microbial biomass. Various protozoa have also been linked to plant growth promotion in many plant species. However, their substrate of choice is bacteria, so selective consumption must account for the proliferation of plant growth promoting bacteria in the presence of bacterivorous protists. Even with this, many researchers have debated whether the increased plant biomass associated with certain rhizosphere protozoa is due to selective grazing of pathogenic bacteria or from the increase of plant hormones resulting from consumption of plant hormone producing bacteria. The protists can also release ammonium by consumption of bacteria, making it available for plants.

Our study demonstrated that the antimicrobial characteristics of P. koreensis JDSCSU. When inoculated into rhizospheres of tomato, the plants were protected tomato from bacterial and fungal phytopathogens. Additionally, inoculation with this pseudomonad offered protection from drought and heat stress. Interestingly, the use of the purified P. koreensis biosurfactant also negated the symptoms of infection typically associated with X. campestris infection on tomatoes. Our research also demonstrated that Pseudomonas koreensis JDSCSU15 produces IAA and siderophores and has the ability to solubilize phosphates. With all of these plant-growth promoting features, the novel pseudomonad has the potential to serve as a biological control and plant growth promotion agent. Other biosurfactanst producing Pseudomonas strains are commercially used as biological controls. P. koreensis JDSCSU15 and its biosurfactant has the potential to be commercially used in the agricultural industry as well.

While this review presented some well-documented examples of PGP bacteria, fungi, and beneficial protozoa, there are other rhizosphere microfauna and viruses that have received less attention and could also positively impact plant growth. While PGPR and PGPF are known to compete with pathogens for nutrients, they may also enhance growth of other beneficial microorganisms. Likewise, the presence of certain protozoa in the rhizosphere has been shown to influence the community composition of PGP bacteria. Additionally, rhizosphere dwelling fungi may also benefit from the presence of nutrient rich remains from partial catabolism of recalcitrant substrates provided by the protozoa and other rhizosphere microbes. In fact, it is likely that all rhizosphere dwelling microorganisms benefit from the remains of partial catabolism by other individuals and inhabit multiorganism consortia, which ultimately benefit the entire microbial community.

Thus, no single organism type is responsible for plant growth promotion. Indeed, the multitrophic interactions among rhizosphere dwelling microorganisms have likely evolved over time to coordinate an increase in the plant biomass, which ultimately leads to increased resources for those microbes. For example, increased plant rooting structures could provide safe habitat and constant access to nutrient rich exudates, which would enhance fitness in many types of microbes.

At this time, the majority of studies on PGP microbes are focused on the relationship between the microbe and the plant. Future work in this field must consider the multitrophic interactions of the rhizosphere dwelling microorganisms. Understanding the relationships between plants, plant growth promoting microbes, and other organisms may help to determine the right cocktail of inoculum for effective biofertilizers. Similarly, PGPR can only be used successfully as biological controls if they can withstand the environment, predation, and competition. Additionally, the benefits of biocontrol strains can be negated if these microbes compete with their intended hosts for nutrients. Thus, the use of PGP microorganisms as phytostimulants can be limited. Conversely, application of biosurfactants or protective VOCs could provide increased growth and protection to plants without the potential of the aforementioned constraints and should continue to be evaluated. Thus, additional study of PGPR microorganisms and their plant protective compounds is warranted as this knowledge could support more sustainable agriculture approaches.

References

Alam S.S., Sakamoto K., Inubushi K. Biocontrol efficiency of fusarium wilt diseases by a root-colonizing fungus Penicillium sp. Soil Science and Plant Nutrition. 2011;57(2):204–212.

Alphei J., Bonkowski M., Scheu S. Protozoa, nematoda and lumbricidae in the rhizosphere of Hordelymu seuropeaus (Poaceae): Faunal interactions, response of microorganisms and effects on plant growth. Oecologia. 1996;106(1):111–126. doi:10.1007/BF00334413.

Arshad M., Shahroona B., Mahmood T. Inoculation with Pseudomonas spp. containing ACC-deaminase partially eliminates the effects of drought stress on growth, yield, and ripening of pea (Pisum sativum L.). Pedosphere. 2008;18(5):611–620.

Barazani O., Benderoth M., Groten K., Kuhlemeier C., Baldwin I.T. Piriformospora indica and Sebacina vermifera increase growth performance at the expense of herbivore resistance in Nicotiana attenuata. Oecologia. 2005;146:234–243. doi:10.1007/s00442-005-0193-2.

Bergsma-Vlami M., Prins M.E., Raaijmakers J.M. Influence of plant species on population dynamics, genotypic diversity and antibiotic production in the rhizosphere by indigenous Pseudomonas spp.. FEMS Microbiology Ecology. 2005;52(1):59–69. doi:10.1016/j.femsec.2004.10.007.

Bitas V., McCartney N., Li N., Demers J., Kim J.E., Kim H.S. Fusarium oxysporum volatiles enhance pant growth via affecting auxin transport and signaling. Frontiers in Microbiology. 2015;6:1248.

Bonkowski M., Brandt F. Do soil protozoa enhance plant growth by hormonal effects?. Soil Biology and Biochemistry. 2002;34:1709–1715.

Bonkowski M., Jentschke G., Scheu S. Contrasting effects of microbes in the rhizosphere: Interactions of mycorrhiza (Paxillus involutus (Batsch) Fr.), naked amoebae (Protozoa), and Norway spruce seedlings (Picea abies karst.). Applied Soil Ecology. 2001;18:193–204.

Compant S., Duffy B., Nowak J., Clement C., Barka A.E. Use of plant growth promoting bacteria for biocontrol of plant diseases: Principles, mechanisms of action, and future prospects. Applied and Environmental Microbiology. 2005;71(9):4951–4959.

D’aes J., Maeyer D.K., Pauwelyn E., Hofte M. Biosurfactants in plant-Psuedomonas interactions and their importance to biocontrol. Environmental Microbiology Reports. 2010;2(3):359–372.

Di X., Takken F.L., Tintor N. How phytohormones shape interactions between plants and the soil-borne fungus Fusarium oxysporum. Frontiers in Plant Science. 2016;7:170. doi:10.3389/fpls.2016.00170.

Ekelund F., Rønn R. Notes on protozoa in agricultural soil with emphasis on heterotrophic flagellates and naked amoebae and their ecology. FEMS Microbiology Reviews. 1994;15(4):321–353. doi:10.1111/j.1574-6976.1994.tb00144.x. 7848658.

Geudens N., Martins J.C. Cyclic lipodepsipeptides from Pseudomonas spp. biological swiss army knives. Frontiers in Microbiology. 2018;9:1867.

Gill S.S., Gill R., Trivedi D.K., Anjum N.A., Sharma K.K., Ansari M.W. Piriformospora indica: Potential and significance in plant stress tolerance. Frontiers in Microbiology. 2016;7:332.

Grady E.N., MacDonald J., Liu L., Richman A., Yuan Z.C. Current knowledge and perspectives of Paenibacillus: A review. Microbial Cell Factories. 2016;15:203.

Haas D., Defago G. Biological control of soil-borne pathogens by fluorescent pseudomonads. Nature Reviews Microbiology. 2005;3:307–319. doi:10.1038/nrmicro1129.

Haichar F.Z., Marol C., Berge O., Rangel-Castro J.I., Prosser J.I., Balesdent J. Plant host habitat and root exudates shape soil bacterial community structure. The ISME Journal. 2008;2:1221–1230.

Hayat R., Ahmed I., Sheirdil R.A. An overview of plant growth promoting rhizobacteria (PGPR) for sustainable agriculture. In: Ashraf M., Öztürk M., Ahmad M., Aksoy A., eds. Crop production for agricultural improvement. Dordrecht: Springer; 2012:557–579. doi:10.1007/978-94-007-4116-4_22.

Hultberg M., Alsberg T., Khalil S., Alsanius B. Suppression of disease in tomato infected by Pythium ultimum with a biosurfactant produced by Pseudomonas koreensis. BioControl. 2010;55:435–444.

Hultberg M., Bengtsson T., Liljeroth E. Late blight on potato is suppressed by the biosurfactant-producing strain Pseudomonas koreensis 2.74 and its biosurfactant. BioControl. 2010;55:543–550.

Hung R., Lee S., Bennett J.W. Arabidopsis thaliana as a model system for testing the effect of Trichoderma volatile organic compounds. Fungal Ecology. 2013;6:19–26. doi:10.1016/j.funeco.2012.09.005.

Hyakumachi M. Plant growth promoting fungi from turfgrass rhizosphere with potential for disease suppression. Soil Microorganisms. 1994;44:53–68.

Jogaiah S., Abdelrahman M., Tran L.S., Shin-ichi I. Characterization of rhizosphere fungi that mediate resistance in tomato against bacterial wilt disease. Journal of Experimental Botany. 2013;64(12):3829–3842.

Khire J.M. Bacterial biosurfactants, and their role in microbial enhanced oil recovery (MEOR). In: Sen R., ed. Biosurfactants. New York: Springer Science & Business Media; 2010:146–157.

Kosaric N., Sukan F. Biosurfactants: Production and utilization—processes, technologies, and economics. FL, USA: CRC Press; 2015. Surfactant science series. (159).

Kottb M.R., Gigolashvili T., Grobkinsky D.K., Piechulla B. Trichoderma volatiles effecting Arabidopsis: From inhibition to protection against phytopathogenic fungi. Frontiers in Microbiology. 2015;8:995. doi:10.3389/fmicb.2015.00995.

Kruijt M., Tran H., Raajimakers J.M. Functional, genetic and chemical characterization of biosurfactants produced by plant growth-promoting Pseudomonas putida 267. Journal of Applied Microbiology. 2009;107:546–556.

Kumar A., Kumar A., Devi S., Patil S., Payal C., Negi S. Isolation, screening and characterization of bacteria from rhizospheric soils for different plant growth promotion (PGP) activities: An in vitro study. Recent Research in Science and Technology. 2012;4(1):1–5.

Kumar V., Menon S., Agarwal H., Gopalakrishnan D. Characterization and optimization of bacterium isolated from soil samples for the production of siderophores. Resource-Efficient Technologies. 2017;3(4):434–439.

Kumar P., Pahal V., Gupta A., Vadhan R., Chandra H., Dubey R.C. Effect of silver nanoparticles and Bacillus cereus LPR2 on the growth of Zea mays. Scientific Reports. 2020;10(1):1–10.

Kuppardt A., Fester T., Härtig C., Chatzinotas A. Rhizosphere protists change metabolite profiles in Zea mays. Frontiers in Microbiology. 2018;9:857. doi:10.3389/fmicb.2018.00857.

Kwon S., Kim J., Park I., Yoon S., Park D., Lim C. Pseudomonas koreensis sp. nov., Pseudomonas umsongensis sp. nov. and Pseudomona sjinjuensis sp. nov., novel species from farm soils in Korea. International Journal of Systematic and Evolutionary Microbiology. 2003;53:21–27.

Li N., Alfiky A., Wang W., Islam M., Nourollahi K., Liu X. Volatile compound-mediated recognition and inhibition between Trichoderma biocontrol agents and Fusarium oxysporum. Frontiers in Microbiology. 2018;9:2614. doi:10.3389/fmicb.2018.02614.

Li N., Kang S. Do volatile compounds produced by Fusarium oxysporum and Verticillium dahliae affect stress tolerance in plants?. Mycology. 2018;9(3):166–175. doi:10.1080/21501203.2018.1448009.

Liu D., Yan R., Fu Y., Wang X., Zhang J., Xiang W. Antifungal, plant growth-promoting, and genomic properties of an endophytic actinobacterium Streptomyces sp. NEAU-S7GS2. Frontiers in Microbiology. 2019;10:2077.

Lozano G.L., Bravo J.I., Handelsman J. Draft genome sequence of Pseudomonas koreensis CL12, a Bacillus cereus hitchhiker from the soybean rhizosphere. Genome Announcements. 2017;5:e00570-17.

Murphy B.R., Doohan F.M., Hodkinson T.R. Fungal root endophytes of a wild barley species increase yield in a nutrient-stressed barley cultivar. Symbiosis. 2015;65(1):1–7.

Myo E.M., Beibei G., Jinjin M., Hailan C., Binghua L., Liming S. Indole-3-acetic acid production by Streptomyces fradiae NKX-259 and its formulation to enhance plant growth. BMC Microbiology. 2019;19:155.

Nautiyal C.S., Srivastava S., Chauhan P.S., Seem K., Mishra A., Sopory S.K. Plant growth-promoting bacteria Bacillus amyloliquefaciens NBRISN13 modulates gene expression profile of leaf and rhizosphere community in rice during salt stress. Plant Physiology and Biochemistry. 2013;66:1–9.

Naziya B., Murali M., Amruthesh K.N. Plant growth-promoting fungi (PGPF) instigate plant growth and induce disease resistance in Capsicum annuum L. upon infection with Colletotrichum capsici (Syd.) Butler & Bisby. Biomolecules. 2020;10:41. doi:10.3390/biom10010041.

Nielsen M.N., Sorensen J. Chitinolytic activity of Pseudomonas fluorescens isolates from barley and sugar beet rhizospheres. FEMS Microbiology Ecology. 1999;30:217–227.

Padda K.P., Puri A., Zeng Q., Chanway C.P., Wu X. Effect of GFP-tagging on nitrogen fixation and plant growth promotion of an endophytic diazotrophic strain of Paenibacillus polymyxa. Botany. 2017;95(9):933–942.

Pal K.K., Tilak K.V.B.R., Saxena A.K., Dey R., Singh S. Suppression of maize root diseases caused by Macrophomina phaseolina, Fusarium moniliforme and Fusarium graminearum by plant growth promoting rhizobacteria. Microbiological Research. 2001;156:209–223.

Park Y.G., Mun B.G., Kang S.M., Hussain A., Shahzad R., Seo C.W. Bacillus aryabhattai SRB02 tolerates oxidative and nitrosative stress and promotes the growth of soybean by modulating the production of phytohormones. PLoS One. 2017;12(3):e0173203.

Raaijmakers J.M., de Bruijn I., de Kock M.J.D. Cyclic lipopeptide production by plant-associated Pseudomonas spp.: Diversity, activity, biosynthesis, and regulation. Molecular Plant-Microbe Interactions. 2006;19:699–710.

Radhakrishnan R., Kang S.M., Baek I.Y., Lee I.J. Characterization of plant growth-promoting traits of Penicillium species against the effects of high soil salinity and root disease. Journal of Plant Interactions. 2014;9(1):754–762.

Roberts E.L., Adamcheck C.A. Interactions between fungal endophtyes and bacterial colonizers of fescue grass. In: Dighton J., J.F.White Jr., eds. The fungal community: Its organization and role in the ecosystem. Boca Raton: CRC Press; 2017:109–118.

Roberts E.L., Ferraro A.R. Rhizosphere microbiome selection by Epichloë endophytes of Festuca arundinacea. Plant and Soil. 2015;396:229–239.

Roberts E.L., Lindow S.E. Loline alkaloid production by fungal endophytes of fescue species select for particular epiphytic bacterial microflora. The ISME Journal. 2014;8:359–368.

Rodríguez M., Torres M., Blanco L., Bejar V., Sampedro I., Llamas I. Plant growth-promoting activity and quorum quenching-mediated biocontrol of bacterial phytopathogens by Pseudomonas segetis strain P6. Scientific Reports. 2020;10:4121. doi:10.1038/s41598-020-61084-1.

Rønn R., Gavito M., Larsen J., Jakobsen I., Frederiksen H., Christensen S. Response of free-living soil protozoa and microorganisms to elevated atmospheric CO2 and presence of mycorrhiza. Soil Biology and Biochemistry. 2002;34(7):923–932. doi:10.1016/s0038-0717(02)00024-x.

Rønn R., McCaig A.E., Griffiths B.S., Prosser J.I. Impact of protozoan grazing on bacterial community structure in soil microcosms. Applied and Environmental Microbiology. 2002;68(12):6094–6105. doi:10.1128/aem.68.12.6094-6105.

Rosenberg K., Bertaux J., Krome K., Hartmann A., Scheu S., Bonkowski M. Soil amoebae rapidly change bacterial community composition in the rhizosphere of Arabidopsis thaliana. The ISME Journal. 2009;3(6):675–684.

Sachdev D.P., Cameotra S.S. Biosurfactants in agriculture. Applied Microbiology and Biotechnology. 2013;97:1005–1016.

Sayyed R.Z., Chincholkar S.B., Reddy M.S., Gangurde N.S., Patel P.R. Siderophore producing PGPR for crop nutrition and phytopathogen suppression. In: Maheshwari D.K., ed. Bacteria in agrobiology: Disease management. Springer; 2013:449–472.

Shaikh S.S., Sayyed R.Z., Reddy M.S. Plant growth-promoting rhizobacteria: An eco-friendly approach for sustainable agroecosystem. In: Hakeem K.R., Akhtar M.S., Abdullah S.N.A., eds. Plant, soil and microbes interactions and implications in crop science. Switzerland: Springer International Publishing; 2016:182–201.

Shi L., Nwet T.T., Ge B., Zhao W., Liu B., Cui H. Antifungal and plant growth-promoting activities of Streptomyces roseoflavus strain NKZ-259. Biological Control. 2018;125:57–64.

Simek K., Vrba J., Pernthaler T., Posch T., Hartman P., Nedoma J. Morphological and compositional shifts in an experimental bacterial community influenced by protists with contrasting feeding modes. Applied and Environmental Microbiology. 1997;63(2):587–595.

Toribio J., Escalante A., Caballero-Mellado J., Gonzalez-Gonzalez A., Zavala S., Souza V. Characterization of a novel biosurfactant producing Pseudomonas koreensis lineage that is endemic to Cuatro Cienegass Basin. Systematic and Applied Microbiology. 2011;34:531–535.

Vyas P., Rahi P., Gulati A. Stress tolerance and genetic variability of phosphate-solubilizing fluorescent Pseudomonas from the cold deserts of the trans-Himalayas. Microbial Ecology. 2009;58(2):425–434. doi:10.1007/s00248-009-9511-2 (.

Weidner S., Latz E., Agaras B., Valverde C., Jousset A. Protozoa stimulate the plant beneficial activity of rhizospheric pseudomonads. Plant and Soil. 2017;410(1–2):509–515.

White J.F., Chen Q., Torres M.S., Mattera R., Irizarry I., Tadych M. Collaboration between grass seedlings and rhizobacteria to scavenge organic nitrogen in soils. AoB Plants. 2015;6:7. doi:10.1093/aobpla/plu093.

Xiong W., Song Y., Yang K., Gu Y., Wei Z., Kowalchuk G.A. Rhizosphere protists are key determinants of plant health. Microbiome. 2020;8(1):27. doi:10.1186/s40168-020-00799-9.

Yadav V., Kumar M., Deep D.K., Kumar H., Sharma R., Tripathi T. A phosphate transporter from the root endophytic fungus Piriformospora indica plays a role in phosphate transport to the host plant. Journal of Biological Chemistry. 2010;285:26532–26544. doi:10.1074/jbc.M110.111021.

Zhang S., Gan Y., Ji W., Xu B., Hou B., Liu J. Mechanisms and characterization of Trichoderma longibrachiatum T6 in suppressing nematodes (Heterodera avenae) in wheat. Frontiers in Plant Science. 2017;8:1491. doi:10.3389/fpls.2017.01491.

Zhang S., Gan Y., Xu B. Application of plant-growth-promoting fungi Trichoderma longibrachiatum t6 enhances tolerance of wheat to salt stress through improvement of antioxidative defense system and gene expression. Frontiers in Plant Science. 2016;7:1405.

Chapter 2: Indigenous nitrogen fixing microbes engineer rhizosphere and enhance nutrient availability and plant growth

Sapna Negia; Pankaj Kumarb; Jitendra Kumarc,d; Ajay Singhe; Ramesh Chandra Dubeyf    a Department of Microbiology and Biotechnology, DBS (PG) College, Dehradun, Uttarakhand, India

b Department of Microbiology, Dolphin (PG) Institute of Biomedical and Natural Sciences, Dehradun, Uttarakhand, India

c Department of Botany, Dolphin (PG) College of Science and Agriculture, Fatehgarh Sahib, Punjab, India

d Department of Biosciences, UIB, Chandigarh University, Mohali, Punjab, India

e Department of Food Technology, Mata Gujri College, Fatehgarh Sahib, Punjab, India

f Department of Botany and Microbiology, Gurukul Kangri Vishwavidyalaya, Haridwar, Uttarakhand, India

Abstract

Nitrogen is the most essential macronutrient for the growth of plants. The current scenario of soil engineering is based on synthetic nitrogen fertilizer and imposing economical as well as environmental stress. Biological nitrogen fixation (BNF) is the only strategy to fulfill the nitrogen demand of plants in a sustainable manner. BNF provides N, which is economic and ecofriendly, reduces the use of chemical fertilizers, and improves the internal resources by engineering the rhizosphere. Indigenous diazotrophs increase the crop productivity, availability or uptake of nutrients through hormonal action or antibiosis. The main objective of rhizosphere engineering is reducing our dependence on agrochemicals by replacing them with ecofriendly beneficial native microbes or introducing the genetically engineered microbes, biostimulants in the soil. Hence, it will help us in developing environment-friendly sustainable agriculture.

Keywords

Nitrogen fixation; Rhizosphere; Nutrient uptake; Chemical fertilizers; nif gene

Chapter outline

2.1Introduction

2.2Nitrogen-fixing microbes

2.3Mechanism of biological nitrogen fixation

2.3.1Symbiotic nitrogen fixation

2.3.2Nonsymbiotic nitrogen fixation

2.4Rhizosphere engineering by N2-fixing microbes

2.5Role of nitrogen-fixing microbes in plant growth enhancement and nutrient uptake

2.6Nitrogen-fixing microbes as biofertilizer for sustainable agriculture

2.7Conclusions

References

2.1: Introduction

Nitrogen is an essential element for plant development and a limiting factor in plant growth. It represents about 2% of the total plant dry matter that enters the food chain (Miller & Cramer, 2005). Nitrogen is abundant in the earth’s atmosphere in the form of N2 gas, but it cannot be used directly by the living organisms to produce chemicals for their growth and reproduction (Wansik et al., 2016). However, there is a continuous depletion of N by some processes, such as soil erosion, chemical volatilization, denitrification, soil leaching, and removal of N-containing crop residues from the land (Vitousek & Matson, 2009). In a wide range of cultivated crops, chemical fertilizers are commonly used to supply the essential nutrients to soil  −  plant systems. The use of high amount of N fertilizer has increased the production cost and causes the significant effects on gross income of small farmers. However, the unscientific use of chemical N fertilizers in the current agricultural systems of industrialized countries has raised environmental concerns (Dal Cortivo et al., 2017). The deleterious effect of chemical fertilizers starts from its manufacturing as the products and byproducts have some toxic chemicals or gases, like NH4, CO2, CH4, etc., which cause air pollution. It also causes water pollution when the untreated wastes from these industries are disposed off into nearby water bodies. Furthermore, soil health and quality also degrades when these effluents are added in soil, hence causing soil pollution. It also increases emissions of greenhouse gases. These chemical fertilizers are not only becoming hazardous for our environment but also adversely affects humans, animals, and microbial life forms (Chandini, Kumar, Kumar, & Prakash, 2019). A study indicates that long-term fertilization adversely affect the diversity, community structure, and assembly processes of soil diazotrophs, which may have implications for the rate of biological N2 fixation in the agricultural systems (Feng et al., 2018). Imbalance in nitrogen cycling, soil physicochemical properties, changing climatic conditions, and abiotic stresses are the major factors that are threatening the sustainable agriculture. Therefore, current trends in agriculture are focusing on the alternative approaches capable of plant growth and crop production by maintaining soil fertility in the natural forms (Fernando, Nakkeeran, & Zhang,