Rhizosphere Bacteria: History
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Contributor:
Qudsia Saeed
,
Wang Xiukang
,
Fasih Ullah Haider
,
Jiří Kučerik
,
Muhammad Zahid Mumtaz
,
Jiri Holatko
,
Munaza Naseem
,
Antonin Kintl
,
Mukkaram Ejaz
,
Muhammad Naveed
,
Martin Brtnicky
,
Adnan Mustafa

Rhizosphere bacterial inoculants are indisputably necessary for the augmentation of plant growth and maintenance of soil output. As reported, rhizosphere bacterial inoculants benefit plants through various mechanisms, although some studies indicate adverse effects. In this entry, the pros and cons of rhizosphere bacterial biofertilizers are compared, and a comparison of such biofertilizers is presented in and demonstrated in.

  • rhizobacteria
  • plant growth
  • abiotic stresses
  • sustainable agriculture
  • plant–microbe interactions

1. Introduction

Recently, crop production has been facing serious threats due to various biotic and abiotic stresses. Feeding the growing population and enhancing agricultural production on limited land are significant challenges for researchers and farmers in the current era [1]. In addition, present agricultural practices, such as the use of fertilizers, pesticides, herbicides, and irrigation with untreated wastewater, pose serious threats to the environment and cause soil degradation [2]. Moreover, urbanization and industrialization have caused a significant reduction in the agricultural area, which has further motivated scientists to develop sustainable strategies to increase crop yields from the already shrinking cropped area [3]. Increasing the area available for crop production has proven difficult; therefore, strategies should be developed to increase the crop yield per unit area in a way that prevents the further degradation of natural resources [4]. Therefore, adopting alternative approaches in today’s agriculture is necessary for ensuring environmental sustainability and future food security.

Several technical strategies suggested in the past involve enhancing agricultural production by reducing agricultural inputs such as fertilizers and pesticides. In this context, the use of rhizobacteria has been increasingly gaining momentum. Rhizobacteria reside in the rhizosphere, and those having beneficial effects on plants are termed plant growth-promoting rhizobacteria [5][6]. These rhizobacteria are equipped with a number of mechanisms (both direct and indirect) through which they improve plant growth in diverse agricultural settings. Several previous studies have reported the natural enhancement of plant growth of field crops by applying plant growth-promoting rhizobacteria (PGPR). The mechanisms for plant growth promotion used by rhizobacteria, which inhabit the rhizosphere, include metabolic adjustments, adjustments in phytohormone levels, production of exopolysaccharides, root colonization, and enhancement of nutrient availability [7][8][9]. These rhizobacteria also indirectly improve plant growth by inducing plant resistance to various biotic and abiotic stresses, such as pathogen attack and heavy metal contamination, using such mechanisms as the production of antibiotics, induction of induced systemic resistance, rhizosphere competence, and production of antagonistic substances for biocontrol [7][10][11][12][13]. Moreover, the mechanisms used by rhizobacteria for the bioremediation of contaminated soils include the production of biosurfactants and siderophores, biosorption, ACC deaminase activity, and production of polymeric substances [14][15][16].

In this entry, the key knowledge of plant growth promotion resulting from rhizosphere bacterial application in diverse agricultural settings is summarized. Here, researchers synthesize the main findings and highlight the in-depth analysis of mechanisms used by rhizobacteria for plant growth promotion, biocontrol, and bioremediation of contaminated sites ( Figure 1 ) in a comprehensive manner. then the pros and cons of rhizobacterial application in modern agriculture for improving plant growth are discussed, and then technical suggestions are evaluated for the future use of rhizobacteria in agriculture.

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Figure 1. An overview of the mechanisms employed by rhizobacteria for plant growth promotion, biocontrol of plant pests, and bioremediation of contaminated soils. BNF, biological nitrogen fixation; ISR, induced systemic resistance; HC, hydrogen cyanide; ACC, 1-aminocyclopropane, 1-carboxylic acid.

2. Plant Growth Promotion by Plant Growth-Promoting Rhizobacteria (PGPR): An Overview

During their development, plants are in intimate and continuous contact with microorganisms present in the root vicinity, known as the rhizosphere. Microbes living in the rhizosphere of several plants and having several positive effects on the host plant through various mechanisms are usually termed plant growth-promoting rhizobacteria (PGPR) [17][18]. In the rhizosphere, plant roots secrete a number of exudates that act as attractants for microbes, which eventually improve the physicochemical properties of the surrounding soil. On the other hand, these exudates maintain the function and structure of microbial communities near plant roots [9][19]. Plants and bacteria form symbiotic associations to alleviate abiotic stresses [20][21][22][23]. PGPR can assist plants in their growth by fixation of atmospheric nitrogen, producing siderophores, generating phytohormones (auxins, gibberellins, cytokinins), solubilizing phosphorus (P), or synthesizing stress-relieving enzymes [24]. Moreover, certain bacteria improve the accessibility of essential nutrients, improve root progression, and lessen stress-induced damage by modifying plant defense systems [25][26]. Furthermore, PGPR indirectly help plant symbionts by initiating induced systemic resistance, exerting an antibiosis effect, and potentially improving the content of plant cell metabolites [25][27]. PGPR can withstand hostile natural conditions such as shortage of water, salt stress, weed invasion, lack of nutrients, and heavy metal pollution [28]. The use of PGPR could help to enhance and improve sustainable agriculture and natural stability. These PGPR can be found in association with roots (in the rhizosphere), which enhance plant growth in the absence of pathogens or lessen the harmful effects of pathogens on crop yield by antibiosis, competition, induced systemic resistance, and siderophore production [29][30][31]. Several mechanisms used by PGPR in plant growth promotion are described in detail in the following section.

3. Plant Growth-Promoting Rhizobacteria (PGPR) as Biocontrol Agents: An Overview

Plant disease outbreaks are a major cause of decreased crop yield, deteriorating production quality, and causing the contamination of food grains. Pesticides have been developed in response to the ever-increasing range and complexity of plant diseases [32][33]. Unfortunately, continued use of these pesticides has resulted in phytopathogen resistance, which raises a number of environmental concerns. Biological control is being considered as an alternative to pesticides for phytopathogen control. [34]. Plant growth and health are assisted by the use of PGPB as biological agents. PGPB have a number of benefits over traditional pest control methods. The use of PGPB in agriculture is both environmentally friendly and non-toxic. PGPB work through a variety of mechanisms to reduce or avoid harm caused by phytopathogens [24].

Plant growth is influenced by PGPR in two ways: indirectly and directly. Direct plant growth promotion by PGPR involves either providing the plant with bacterium-produced compounds, such as phytohormones, or promoting the absorption of certain nutrients from the environment [35]. As PGPR reduce or prevent the negative effects of one or more phytopathogenic species, they indirectly promote plant growth. This can be accomplished by generating antagonistic compounds or inducing pathogen resistance [35]. One or more of these mechanisms can be used by a specific PGPR to influence plant growth and development.

PGPR may function as biocontrol agents via a variety of mechanisms ( Table 1 ) irrespective of their position in plant growth enhancement, such as the establishment of auxin phytohormone development [36], reduction in plant ethylene levels [37], or nitrogen fixation [38]. Plant– PGPR interactions are commercially exploited [39], and they hold great promise for long-term agriculture. A number of commercial and food crops have been studied in relation to these associations [40].

Table 1. Summary of studies on rhizobacterial mechanisms involved in biocontrol.
Biocontrol Agent Plant Pathogen Host Plant Proposed Mechanism(s) Reference
Pseudomonas fluorescens Fusarium culmorum Rye Fe(III)-chelating compounds (including siderophores) [41]
Acinetobacter, Pseudomonas, Staphylococcus, Bacillus, Enterobacter, Pantoea, Alcaligenes Fusarium oxysporum, Alternaria alternate, F. culmorum, F. solani, Botrytis cinerea, Pythium ultimum, Phytophthora cryptogea Wheat Antagonism and growth promotion [37]
Bacillus sp. L324-92 Gaeumannomyces graminis var tritici, Rhizoctonia root rot, R. solani AG8, Pythium root rot, Pythium irregulare P. ultimum. Wheat Not specified [42]
Bacillus sp., Pseudomonas fluorescens R. oryzae, P. ultimum, G. graminis, R. solani Wheat Not specified [43]
Pseudomonas fluorescens Microconidium nivale/ Fusarium nivale Wheat Growth promotion, siderophore production, in vitro antibiosis [44]
Bacillus subtilis and B. cereus Take all (G. graminis var tritici) Rhizoctonia root rot (R. solaniAG8) Wheat Growth promotion [45]
Bacillus subtilis CE1 Fusarium verticillioides Maize Not specified [46]
Pseudomonas chlororaphis Macrophomina phaseolina (charcoal rot of sorghum) Sorghum Extracellular antibiotics, production of volatiles, siderophores, effective root colonization [47]
Pseudomonas fluorescens MKB 100 and MKB 249, P. frederiksbergensis 202, Pseudomonas spp. MKB 158 Fusarium culmorum Wheat and barley Induced resistance, antibiotic production, pathogenesis-related proteins (induced resistance) in wheat [165

The use of bacteriophage as a biocontrol agent has been a promising yet uncommon technique in recent years. Phages have the inherent ability to address phage resistance or new bacterial strains and are compatible with a variety of other biocontrol agents. Because of their sensitivity to UV light, they must be sprayed on the plant in the evening [48]. They can be used in phage-based diagnostics of phytopathogenic bacteria in addition to being used as biocontrol agents.

4. Pros and Cons of Rhizosphere Bacteria for Agricultural Sustainability

Rhizosphere bacterial inoculants are indisputably necessary for the augmentation of plant growth and maintenance of soil output. As reported in the above sections, rhizosphere bacterial inoculants benefit plants through various mechanisms, although some studies indicate adverse effects [5]. In this section, the pros and cons of rhizosphere bacterial biofertilizers are compared, and a comparison of such biofertilizers is presented in Table 2 and demonstrated in Figure 2 .

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Figure 2. Comparison of pros and cons of rhizobacterial application for sustainable agriculture with possible future directions [49][50][51][52][53][54].

Numerous commercially available microbial biofertilizers are sold as dried or liquid cultures under a variety of trade names, as listed in Table 2. The application of such rhizosphere bacterial biofertilizers could have an impact on agricultural sustainability and phytopathogen biocontrol and sustain soil and plant production by improving nutrient availability and reducing the application of chemical fertilizers and pesticides. The bioremediation and biodegradation of hazardous substances of biological or anthropogenic origin could also be improved [55]. Various beneficial rhizosphere bacterial inoculants could be formulated in the form of products, including biofertilizers. Such products are viable sources of nutrients that could act as alternatives to chemical fertilizers, stimulate plant growth, remediate heavy metal-contaminated environments, and mitigate environmental stresses [56][57].

Table 2. Pros of biofertilizers and their composition.
Pro’s Types Product (Bacterial Composition) References
Nitrogen fixers AgriLife NitroFix (A. chroococcum, A. vinelandii, A. diazotrophicus, A. lipoferum, R. japonicum), Ajay Azospirillum (Azospirillum sp.), Azofer (A. brasilense), Azo-N (A. brasilense + A. lipoferum), Azo-N Plus (A. brasilense + A. lipoferum + A. chroococcum), Azoter (A. chroococcum, A. brasilense, B. megaterium), Azotobacterin (A. brasilense B-4485), BactoFil A10 (B. Megaterium + A. brasilense, A. vinelandii), BactoFil Soya (B. japonicum), BiAgro 10 (B. japonicum), Bioboots (Bradyrhizobium sp. + D. acidovorans), Biofix (Rhizobia), BioGro (C. freundii, K. pneumoniae, P. fluorescens), Bio-N (Azospirillum spp.), Cell-Tech (Rhizobia), Custom N2 (P. polymyxa), Dimargon (A. chroococcum), Legume Fix (B. japonicum + Rhizobium sp.), Mamezo (Rhizobia), Nitragin Gold (Rhizobia), Nitrasec (Rhizobium sp.), Nitrofix (Azospirillum sp.), Nodulator (B. Japonicum), Nodulator PRO (B. subtilis + B. Japonicum), Nodulest 10 (B. japonicum), Nodumax (Bradyrhizobium spp.), Phylazonit M (A. chroococcum + B. megaterium), Rhizofer (R. etli), Rhizosum Aqua (Azospirillum sp.), Rhizosum N (A. vinelandii + R. irregularis), Rizo-Liq (Bradyrhizobium sp., + M. ciceri, + Rhizobium spp.), Rizo-Liq Top (B. japonicum), Symbion N (Azospirillum sp. + Rhizobium sp. + Acetobacter sp. + Azotobacter sp.), TagTeam (P. bilaii + Rhizobia), TwinN and TripleN (Azorhizobium sp. + Azoarcus sp. + Azospirillum sp.), Zadspirillum (A. brasilense), [11][49][50][58][59][60][61][62][63]
Nutrient solubilizers Bio Phos (B. megaterium), Biozink (PGPR consortia), CataPult (Bacillus spp. + G. intraradices), CBF (B. mucilaginosus, + B. subtilis), Fosforina (P. Fluorescens), K Sol B (F. aurantia), P Sol B (P. striata, + B. polymyxa, B. megaterium), Phosphobacterin (B. megaterium), Rhizosum K (F. aurantia), Rhizosum PK (B. megaterium, + F. aurantia, + R. irregularis), Symbion van Plus (B. megaterium), Zn Sol B (T. thiooxidans), [50][59][60][63][64]
Biopesticides Biobit, Dipel, and Delfin (Bacillus thuringiensis var. kurstaki), Certan (Bacillus thuringiensis var. aizawai), Acrobe, Skectal, Vectobac (Bacillus thuringiensis var. israelensis), Trident, Novodor (Bacillus thuringiensis var. tenebrionis), Ciba-Foil, Agree, Cutlass (Bacillus thuringiensis var. conjugates), MVP, M-Trak (Pseudomonas fluorescens (Bt toxin), Doom (Bacillus papilliae), Invade (Serratia entomophila) [65][66][67]
Other biofertilizers Amase (P. azotoformans), Bioativo (PGPR consortia), EVL Coating (PGPR consortia), Biotilis (B. subtilis), Cedomon (P. chlororaphis), Cedress (P. chlororaphis) [50][59]

The shelf life of biofertilizers and the commercialization of a successful rhizosphere bacterial inoculant remain as major challenges [68]. Biofertilizers with a short shelf life need to be recycled before expiration, which results in financial losses for the associated firm. Their storage and transportation require additional caution because biofertilizers are composed of live bacterial cells and can deteriorate under harsh environmental conditions [64]. A mutation in a bioinoculant may create a serious problem if it decreases its efficiency and thus raises the cost of production. To increase the shelf life of biofertilizers, a suitable carrier is needed for field application. The lack of a suitable carrier is a significant restriction on its widespread usage in fields. Peat, charcoal, and lignite are considered excellent carriers for biofertilizer processing; however, the majority are in short supply in developing countries, and mining of these carriers has been downscaled in developed countries. A potential carrier should be inexpensive, nearly sterile, and free from moisture and toxic substances in addition to having both high organic matter content and water-holding capacity [52]. At the moment, there are no quality control procedures for biofertilizers. It is necessary to develop quality control standards for biofertilizers to demonstrate their efficacy in promoting plant growth on a field scale [64].

Farmers are skeptical of biofertilizers due to the extremely slow and frequently unsuccessful crop responses to applied biofertilizers, as the inoculum requires a longer time to colonize the roots and for the effective concentration to be established. Biofertilizer efficacy is reduced in the field due to the residual properties of harmful chemicals [64]. Environmental stresses contribute significantly to the reduction in biological activity in some areas. Several other factors contributing to the poor performance of biofertilizers include nutrient availability, soil acidity and alkalinity, high and low temperatures, pesticide application, radiation, and high nitrate concentrations in the soil, which limit the bioinoculants’ ability to fix atmospheric N, solubilize nutrients, and interact with indigenous soil microbiota, which influences the presence and survivability of rhizosphere bacteria and the host plant [69]. Numerous soils are contaminated with heavy metals as well as deficient in other critical nutrients, which reduce the biological potential of rhizosphere bacterial inoculants in biofertilizers [70]. Region-specific rhizosphere bacterial biofertilizers should be identified to optimize the effectiveness of the used strains. Soil fumigation with broad-spectrum biocidal fumigants has a deleterious effect on the soil microbial community [71]. The inconsistent application of biofertilizer limits the presence of viable bacterial populations, which results in their inefficiency in promoting the growth of agronomic crops. Typically, farmers expect rapid, visible outcomes from a single application of biofertilizers, which represents another serious limitation to their wide-scale application. The limited application of biofertilizer could be due to the lack of awareness in farmers about the concentration, time, and method of biofertilizer application. Repeated applications of biofertilizer are needed to maintain the bacterial numbers and ensure a viable PGP rhizobacterial population in soil for alleviating various environmental stresses. However, the literature is limited in specifying the required biofertilizer dosage. Therefore, extensive research is required to evaluate the optimal dose of biofertilizers and their effects on crop productivity and stress alleviation.

This entry is adapted from the peer-reviewed paper 10.3390/ijms221910529

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