Pesticides, Microbial

E. Montesinos , A. Bonaterra , in Encyclopedia of Microbiology (Third Edition), 2009

Microorganisms Active in the Biological Control of Plant Pathogens and Their Mechanism of Action

Finding beneficial microorganisms to develop microbial pesticides is a trial-and-error process. The experience accumulated over several decades of research using different screening strategies indicates that many suitable sources come from disease-suppressive soils or healthy plants in epidemic areas affected by a given disease. However, success has also been obtained with nondirected search, that is finding microorganisms of interest from habitats far from the plant environment intended to be protected.

To be a biological control agent is not an attribute of a given genera or species of microorganisms, but it is generally restricted to the strain level. Usually, a few out of the thousands of strains that have been isolated result in a good candidate being developed as a commercial biopesticide. Many research projects have been successful and hundreds of strains of microorganisms have been reported as active in the control of plant pathogens, such as bacteria and fungi causing aerial or root diseases, or are effective against postharvest rot of products like fresh fruits and vegetables. Strains of biological control agents are distributed among Gram-negative bacteria of the families Rhizobiaceae, Pseudomonadaceae, and Enterobacteriaceae, and among Gram-positive bacteria such as Bacillaceae, Lactobacillaceae, Leuconostocaceae, and Streptomycetaceae. There are also representatives of yeasts and fungi within Ascomycota and Basidiomycota, and also in Oomycota. Finally, there are also hipovirulent pathogens with biocontrol ability like Fusarium, Rhizoctonia, Sclerotinia, and Phytophthora, mainly isolated from suppressive soils ( Table 1 ).

Table 1. Groups of microorganisms that have strains of biocontrol agents of plant diseases

Group Family/Phylum Genus
Bacteria Bacillaceae Bacillus
Paenibacillaceae Brevibacillus
Paenibacillus
Cellulomonadaceae Cellulomonas
Enterobacteriaceae Enterobacter
Pantoea (Erwinia)
Rahnella
Serratia
Lactobacillaceae Lactobacillus
Leuconostocaceae Leuconostoc
Pseudomonadaceae Burkholderia
Pseudomonas
Rhizobiaceae Agrobacterium
Streptomycetaceae Streptomyces
Yeast Ascomycota Aureobasidium
Candida
Coniothyrium
Debaryomyces
Kloeckera
Metschnikowia
Pichia
Basidiomycota Cryptococcus
Pseudozyma
Rhodotorula
Sporobolomyces
Fungi (molds) Ascomycota Ampelomyces
Chaetomium
Epicoccum
Gliocladium
Muscodor
Myrothecium
Penicillium
Trichoderma
Ulocladium
Basidiomycota Phlebiopsis
Oomycota Pythium

Beneficial microorganisms able to control plant diseases can colonize or compete with the pathogens for nutrients and sites of interaction, or exert antagonism through antimicrobial compounds, develop hyperparasitism or directly attach to the pathogen cells, interfere with pathogen signals, or induce resistance into the plant host. There are examples of strains that cover a single mechanism, or it is possible that a combination of several mechanisms converge within the same strain ( Table 2 ; Figures 3 and 4 ). Antibiosis against plant-pathogenic bacteria and fungi is very common among bacterial pesticides, for example, by the production of opines, a type of toxic derivative of amino acids, in Agrobacterium radiobacter, phenolic antifungal compounds in Pseudomonas species, antimicrobial peptides and polyenes in Bacillus and actinomycetes, or lytic enzymes in several yeast and fungi like Candida and Trichoderma. Competitive exclusion of the pathogen from sites of infection by better use of nutrients and colonization is also a common mechanism that can accompany other mechanisms. Several hyperparasites, especially abundant among the yeast and fungi biocontrol agents like Coniothyrium, Gliocladium, Pichia, Ampelomyces, Streptomyces, and Trichoderma, interact directly and degrade the fungal cell wall or spore envelope. Some bacteria and fungi are able to induce defense responses in plants, by producing either elicitors (e.g., cell wall components) or messenger molecules (e.g., salicylic acid). Finally, a new mechanism has emerged based on the finding that there are bacteria that can degrade chemical signal messengers necessary for quorum sensing (e.g., acyl homoserine lactones) used by many plant–pathogenic bacteria pathogens to start the infection process in the host.

Table 2. Mechanisms of action in selected biocontrol agents of plant diseases

Microorganism and strain Target pathogen or disease Mechanism involved
Virus
  Bacteriophage Xanthomonas and Pseudomonas diseases Lysis
Bacteria
  A. radiobacter K84/K1026 A. tumefaciens Ab-opines
  B. amyloliquefaciens FZB42 Fusarium oxysporum Ab-AMP
  B. subtilis ATCC6633 Pythium Ab-AMP
  B. subtilis 6051 P. syringae Ab-AMP
  B. subtilis GA1 Botrytis Ab-AMP
  B. subtilis UMAF6614 Podosphaera fusca Ab-AMP
  P. agglomerans Eh318/C9-1 Fire blight CE, Ab-pseudopeptide
  P. agglomerans EPS125/CPA-2 Postharvest fungi CE
  P. chlororaphis PCL1391 F. oxysporum Ab-PCA
  P. chlororaphis MA342 Pythium, others Ab-DDR, CE
  P. fluorescens A506 Fire blight and frost damage CE, Ab
  P. fluorescens Pf-5 Pythium, Rhizoctonia Ab-DAPG, Plt, Prn
  P. fluorescens Q2-87 Gaeummanomyces graminis Ab-DAPG
  P. fluorescens WCS417 F. oxysporum IR
  P. fluorescens SS101 Phytophthora Ab-cAMP, IR
  P. fluorescens EPS62 E. amylovora CE
  P. syringae ESC10/ESC11 Postharvest rot fungi Ab-Syr, CE
  S. griseoviridis K61 Soil-borne pathogens CE, HP, Ab-polyenes
Fungi
  Ampelomyces quisqualis AQ10 Powdery mildew HP
  A. pullulans CF10 Postharvest fungi, fire blight CE, Ab
  A. pullulans Ach1-1 Postharvest fungi CE
  C. oleophila I-182/Q Postharvest fungi CE, Ab-lytic enzymes
  C. sake CPA-1 Postharvest fungi CE
  Coniothyrium minitans CON/M/91-08 Fungi HP
  Gliocladium catenulatum J1446 Soil-borne fungal pathogens HP, Ab-lytic enzymes
  G. virens GL21 Soil-borne fungal pathogens HP, Ab-gliotoxin
  P. guilliermondii 87 Fungi CE, HP
  T. harzianum T22, P1 Soil-borne pathogens COM

Ab, antibiosis; AMP, cyclic antimicrobial peptides; CE, competitive exclusion; COM, complex; DAPG, diacetyl phloroglucinol; DDR, didehydro-rhizoxin; HP, hyperparasitism; IR, induced resistance; PCA, phenylcarboxilic acid; Plt, pyoluteorin; Prn, pyrrolnitrin; Syr, syringomicin.

Figure 3. An overview of the mechanisms of biological control of plant pathogens that have been demonstrated in beneficial microorganisms interacting with plants.

Figure 4. Antagonism against plant pathogens can be revealed in vitro. (a) Halus of inhibition of confluent growth of a fungus produced by colonies of selected antagonistic bacteria and yeast. (b) Antibiosis is accompanied by swarming motility of the colonies of the antagonist bacteria against a plant-pathogenic bacterium. (c) Production of lytic enzymes that hydrolyze chitin, a component of the fungal cell wall that has been added to the agar plate. (d) Synthesis of siderophores around colonies that are involved in competition for iron. (e, f) Direct interference and hyperparasitism due to attachment of bacterial cells to the spores of fungi.

The basic and applied research on biological control agents has stimulated sequencing of their genomes. The genome has been completely sequenced for various biological control strains like Bacillus amyloliquefaciens FZB42 (3.9   Mb), Bacillus subtilis 168 (4.21   Mb), and P. fluorescens Pf-5 (7.1   Mb). In the case of fungal strains, the genome sequence is available for Debaryomyces hansenii (7 chromosomes and 12.2   Mb) and Pichia guilliermondii (10.54   Mb), which have strains that control several postharvest and preharvest fungi. Sequencing is in progress for Trichoderma atroviride (40   Mb), which has strains that can serve as general-purpose microbial biopesticides.

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Volume 3

E. Arias-Roth , ... C. Delbès , in Encyclopedia of Dairy Sciences (Third Edition), 2022

Food Safety Aspects

Besides beneficial microorganisms, raw milk may contain a variety of pathogenic bacteria and bacteria having a controversial safety status, for example, enterococci exhibiting antibiotic resistance, and bacteria producing biogenic amines. Survival of pathogens present in raw milk is greatly dependent upon the technology applied to cheese processing. The acidification rate and the temperature–time profile of the whole process, including ripening, as well as the moisture and salt contents constitute the main factors affecting the survival and growth of pathogens in cheese. As a consequence of the prevalence in raw milk, and the survival and growth potential during cheesemaking and cheese ripening ( D-value, growth temperature range, tolerance to acids and salt), the pathogens most frequently found in raw milk cheeses are enterotoxin-producing Staphylococcus aureus, verotoxin-producing Escherichia coli (VTEC), L. monocytogenes, and Salmonella spp. This is a great safety concern, as consumption of even low numbers of Salmonella spp. or pathogenic E. coli (10–100   cfu per serving) and medium numbers of L. monocytogenes (104–105  cfu per serving) may induce disease. In particular, surface-ripened cheeses are the most susceptible to psychrotrophic L. monocytogenes contamination on the surface (due to the pH close to neutral), during both ripening and storage at cool temperatures. Contamination of milk with S. aureus is usually associated with udder infections. Poor-quality raw milk may contain several thousand per mL, and, consequently, fresh curd produced from such milk may have an S. aureus count of more than 105  g−1 due to growth and passive enrichment in the cheese matrix. If the count of S. aureus exceeds 105  cfu   g−1, significant amounts of staphylococcal enterotoxins (SET) may be formed, which will persist in the curd for months although the bacteria themselves substantially decrease in number during cheese ripening. The European Regulation (EC) No. 2073/2005 on microbiological criteria for foodstuffs has set down process hygiene criteria for coagulase-positive staphylococci, requiring examination of the product at the times during the manufacturing process when the number of staphylococci is expected to be highest. In 2019 Commission Regulation (EU) 2019/229, amending EC Regulation (EC) No 2073/2005, has been published.

Extra-hard and hard cheeses made from raw milk, such as Parmigiano Reggiano, Gruyère, Comté, and Emmentaler, are considered to be free from viable pathogens, as hard cheeses combine a series of hurdles that prevent their survival, namely, high temperature applied during cooking and pressing, low pH and moisture content, and longer minimum ripening periods in the range of 4–18 months. Nevertheless, on the surface of extra-hard and hard cheeses, recontamination with pathogens (e.g., L. monocytogenes) must be prevented.

Semi-hard cheeses are more susceptible to contamination with pathogens as the temperatures applied during production are closer to the growth optimum. Pathogens such as S. aureus, E. coli, or Salmonella spp. can be controlled if the contamination of the vat milk is kept low and if rapid acid production is ensured by the addition of an active starter. L. monocytogenes, which may be present in raw milk, is hardly inactivated during the manufacture and ripening of semi-hard cheese. Therefore, regular examination of milk, as well as of cheese rind samples, is an important measure to control L. monocytogenes in semi-hard raw milk cheese.

Soft cheeses are very susceptible to contamination by L. monocytogenes, Salmonella spp. S. aureus and E. coli. Soft cheeses are manufactured as short-ripened small loaves, making them prone to extensive deacidification by surface microflora. Together with the fact that soft cheeses may contain residual sugars, depending upon the technology applied, this establishes inviting conditions for these pathogens with better survival on the rind compared to the cheese core, and even growth. Because soft cheeses are generally consumed with the rind, monitoring of both raw milk and the finished product at an increased frequency compared to other cheese types is a key element of the strategy ensuring food safety of these products.

As a primary means of food safety, milk is often treated by pasteurization, thermization, or microfiltration to eliminate or reduce the concentration of pathogenic bacteria present in the vat milk. However, the incidence of outbreaks associated with cheese consumption and the occurrence of contaminated cheese on the market are not higher for raw milk cheeses than for pasteurized milk cheeses. In the United States, all listeriosis outbreaks leading to fatal outcomes were linked to recontamination of pasteurized cheeses (Costard et al., 2017). In Europe, a high safety level is primarily achieved by the implementation of comprehensive HACCP concepts in cheese factories processing raw milk, and monitoring programs based upon legally defined food safety criteria and process hygiene criteria. Some countries disregard the fact that a high food safety standard can be obtained in raw milk cheeses, and require the labeling of all cheeses made from unpasteurized milk with special health alerts (Fig. 3). In the United States, the regulations of the Food and Drug Administration (FDA) require all cheeses made from unpasteurized milk to be aged at least 60 days before being sold. As a consequence, traditional soft cheeses such as Brie de Meaux and Camembert de Normandie are available on the US market in the form of cheese made from pasteurized milk.

Fig. 3. Example of labeling of raw milk cheeses with health alerts.

Heat treatments reduce the risk of occurrence of pathogens in the vat milk but simultaneously reduce the biodiversity of the flora present in the final cheese. Raw milk cheeses harbor a complex flora acting as a protective barrier against pathogens (Montel et al., 2014), whereas pasteurized milk cheeses are much more susceptible to post-pasteurization contamination, for example to contamination by E. coli and L. monocytogenes, typically occurring in ripening facilities or during cutting at the retail premises. Moderate heat treatments such as thermization may select for heat-resistant microorganisms (e.g., Enterococci, M. tuberculosis, C. burnetii), by enabling survival while reducing competitive flora.

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Disease and Biosecurity

David I. Prangnell , Tzachi M. Samocha , in Sustainable Biofloc Systems for Marine Shrimp, 2019

12.3.3 Probiotics

Probiotics are beneficial microorganisms added to a tank to prevent pathogenic viruses and bacteria such as Vibrio spp. from becoming established (Lakshmi et al., 2013; see Section 6.5). These beneficial bacteria compete with pathogens to limit their growth, improve water quality, or improve shrimp health and immune response (Hai and Fotedar, 2010).

Probiotics are recommended in biofloc systems and are effective in controlling Vibrio infections in Pacific White Shrimp (Balcázar et al., 2007; Krummenauer et al., 2014). When using feeds that do not have probiotics, they can be added directly to the culture water or sprayed on feed. There are many detailed reviews of probiotics in shrimp aquaculture, including types, sources, application methods, modes of action, selection, and safety (Cruz et al., 2012; Hai and Fotedar, 2010; Lakshmi et al., 2013).

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Selection of New Probiotics: The Case of Streptomyces

Sneha Hariharan , Selvakumar Dharmaraj , in Therapeutic, Probiotic, and Unconventional Foods, 2018

2.1 Definition

Probiotics are beneficial microorganisms, or their products, that provide health benefits to the hosts. These probiotics has been used in aquaculture as disease control agents, or as feed supplements, to improve growth and in some cases, as a means of replacing antimicrobial compounds ( Moriarty, 1997; Dharmaraj and Dhevendaran, 2010). Much research has been carried out in the field of probiotics over the past 30 years, but the original idea was possibly formed by Metchnikoff in the early 1900s. Metchnikoff (1907) theorized that human health could be aided through the ingestion of fermented milk products. The word "probiotic" was introduced by Parker (1974), who defined it as "organisms and substances which contribute to intestinal microbial balance." The term probiotic means "for life," originating from the Greek words "pro" and "bios" (Gismondo et al., 1999). According to Browdy (1998), one of the most significant technologies that evolved in response to disease control problems is the use of probiotics. Probiotics are live microbes that can be used to improve the host intestinal microbial balance and growth performance. Development of probiotics in aquaculture management will reduce the prophylactive use of antimicrobial drugs, as the recent overdependence on the antimicrobial drugs poses potential hazards to people who consume them (Salminen et al., 1999).

Fuller (1989) proposed the widely accepted definition for probiotics, which he gives as "a live microbial feed supplement which beneficially affects the host animal by improving its intestinal microbial balance." Fuller's definition was a revision of the original probiotic concept which referred to protozoans producing substances that stimulated other protozoans (Lilly and Stillwell, 1965). Several modifications were put forward to shorten the definition for probiotics (Gram et al., 1999; Irianto and Austin, 2002a,b). Verschuere et al. (2000) proposed a definition which states that "a live microbial adjunct which has a beneficial effect on the host by modifying the host associated or ambient microbial community, by ensuring improved use of the feed or enhancing its nutritional value, by enhancing the host response towards disease, or by improving the quality of its ambient environment." Kesarcodi-Watson et al. (2008) defined it as "it should benefit the host either nutritionally or by changing its immediate environment." Current probiotic applications and scientific data on mechanisms of action indicate that nonviable microbial components act in a beneficial manner, and this benefit is not limited just to the intestinal region (Salminen et al., 1999). The concept of probiotic activity has its origins in the knowledge that active modulation of the gastrointestinal tract (GIT) could confer antagonism against pathogens, help development of the immune system, provide nutritional benefits, and assist the intestinal mucosal barrier (Vaughan et al., 2002).

Today probiotics are quite commonplace in health-promoting "functional foods" for humans, as well as therapeutic, prophylactic, and growth supplements in animal production and human health (Senok et al., 2005). Multiple ways exist in which probiotics could be beneficial, and these could act either singly or in combination for a single probiotic. These include: inhibition of a pathogen via production of antagonistic compounds, competition for attachment sites, competition for nutrients, alterations of enzymatic activity of pathogens, immune-stimulatory functions, and nutritional benefits such as improving feed digestibility and feed utilization (Bomba et al., 2002). It is often reported that a probiotic must be adherent and colonize within the GIT, replicate to high numbers, produce antimicrobial substances, and withstand the acidic environment of the GIT (Dunne et al., 1999; Mombelli and Gismondo, 2000). However, these descriptions are misleading. These beliefs are based on the understanding that a probiotic must become a permanent member of the intestinal flora. While bacteria with this capacity are common, and much probiotic research focuses on attachment capacity of bacteria, it has actually been demonstrated that transient bacteria can also exert beneficial effects (Isolauri et al., 2004). Additionally, contrary to the requisite of being able to attach to mucus and produce antimicrobial substances, a probiotic need only possess one mode of action. Multistrain and multispecies probiotics have proven that it is possible to provide synergistic bacteria with complementary modes of action to enhance protection (Timmerman et al., 2004).

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Smart Fertilizers as a Strategy for Sustainable Agriculture

Marcela Calabi-Floody , ... Maria de la Luz Mora , in Advances in Agronomy, 2018

3.2 Bioformulation Fertilizer: Plant Growth Promoting and Nutrient Use Efficiency

One group of microorganisms beneficial for plant growth is PGPR, a heterogeneous group of bacteria that can be found in the rhizosphere, at root surfaces, and in association with roots (Ahmad et al., 2008). These bacteria have several functions, including production and regulation of phytohormones, release of nutrients to plants (e.g., P-, N-fixation, siderophores, among others), and control of phytopathogens (production of antibiotics and siderophores) (Egamberdieva and Adesemoye, 2016; Martínez-Viveros et al., 2010; Zahid et al., 2015).

Phosphobacteria, phytate-mineralizing bacteria, and phosphate-solubilizing bacteria have been commonly isolated from soil and proposed as inoculants for agricultural improvement (Jorquera et al., 2008). For example, a large diversity of microbes in Andisols under pastures and cereal crops are capable of mineralizing phytate (Jorquera et al., 2008; Martínez-Viveros et al., 2010; Menezes-Blackburn et al., 2014). They may be used to develop bacterial or enzyme systems as biofertilizers to overcome the limitations of conventional fertilizers in acidic soils, as well as for developing added value products from agricultural wastes. To this end, Calabi-Floody et al. (2012) studied the effect of enzyme–nanoclay complexes on P availability of composted cattle dung and showed that it increased the inorganic P content. Moreover, Menezes-Blackburn et al. (2014) suggest that inoculation of cattle manure with enzyme–nanoclay complexes enhances the organic P cycling and P nutrition of plants grown in P-deficient soils.

Low N acquisition by plants is a limiting factor in agricultural ecosystems, and there is interest in using N2-fixing bacteria as an alternative to conventional fertilization. Diazotrophic bacteria are capable of converting atmospheric dinitrogen (N2) into NH3, which can be used by plants (Islam et al., 2009). Among them, a number of free-living soil bacteria are considered to be PGPR because of their competitive advantage in C-rich and N-poor environments (Kennedy et al., 2004). Free-living N2-fixing bacteria have been considered as an alternative to conventional N fertilizer for promoting plant growth, and several research studies reported significant increases in grain and shoot biomass yield from plants inoculated with free-living diazotrophic bacteria (Andrade et al., 2013; Barua et al., 2012; Kennedy et al., 2004; Park et al., 2005). Moreover, Vadakattu and Paterson (2006) reported that under intensive wheat rotation at Avon, South Australia, free-living N2-fixing bacteria contributed 20   kg N per ha per year, which represented 30%–50% of total crop requirements. This response was attributed to a combination of factors including enhancement of root development, production of growth regulators, and N2-fixation (Naiman et al., 2009). However, it is well known that bacteria directly inoculated in the soil system could be adversely affected by competition with native microorganisms, unfavorable physicochemical conditions, and fluctuating pH and temperature (Bréant et al., 2002).

Encapsulating microorganisms in carrier materials (bioformulation) is designed to protect them during storage and from adverse environmental condition (pH, temperature, etc.) (Fig. 4B), thus ensuring a gradual and prolonged release (Bashan, 1986; Kim et al., 2012). A wide range of microorganisms have been investigated, and a framework for selecting suitable organisms for specific purposes has been developed (Table 2).

Table 2. Quality Criteria of Carriers for the Development of Smart Fertilizers Based on Microbial Inoculants

Quality Criteria of Model Carriers of Bioformulations References
High water-holding and water-retention capacity and suitable for as many bacteria as possible/cost effective Mishra and Dahich (2010)
Free from lump-forming material/near sterile or easy to sterilize by autoclaving or by other methods like gamma irradiation/nearly neutral pH or easily adjustable and good pH buffering capacity Keyser et al. (1993)
Available in adequate amounts/nontoxic in nature Bazilah et al. (2011)
For carriers used for seed treatment, should assure the survival of the inoculants on the seed since normally seeds are not immediately sown after seed coating Muresu et al. (2003)
For carriers that shall be used for seed coating, should have a good adhesion to seeds Hegde and Brahmaprakash (1992)
No heat of wetting/easily biodegradable and nonpolluting/supports growth and survival of bacteria/amenable to nutrient supplement/manageable in mixing, curing, and packaging operations Smith (1992)
Chemically and physically uniform Bashan (1998)
The inoculant should be nontoxic, biodegradable, and nonpolluting, and should minimize environmental risks such as the dispersal of cells to the atmosphere or to the ground water Bashan (1998)

Adapted from Sahu, P.K., Brahmaprakash, G.P., 2016. Formulations of biofertilizers—approaches and advances. In: Singh, D.P., Singh, H.B., Prabha, R. (Eds.), Microbial Inoculants in Sustainable Agricultural Productivity—vol. 2: Functional Applications. Springer, pp. 179–198.

Materials suitable for immobilization and preservation of bacteria include alginate gels, synthetic gels (Sol–Gel), polyacrylamide, agar and agarose, polyurethane, vermiculite, and polysaccharides (Bashan, 1998; Liu et al., 2008). In addition, composite materials based on biodegradable polymer clay or nanoclays are being studied, including nanocomposites (Calabi-Floody et al., 2009). For example, encapsulation of free-living diazotrophic bacteria has been considered as one of the possible alternatives for inorganic N fertilizer for promoting plant growth and crop yield (Ivanova et al., 2005).

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Physiological and molecular mechanisms in improving salinity stress tolerance by beneficial microorganisms in plants

Şeyma Arıkan , ... Ahmet Eşitken , in Microbial Management of Plant Stresses, 2021

Abstract

Through symbiotic and asymbiotic interactions, beneficial microorganisms promote plant growth and development directly or indirectly according to their unique abilities. These microorganisms produce plant growth regulators, including ACC-deaminase and siderophore, those that release organic acids, N 2-fixing bacteria and phosphate solubilizing bacteria, and those that increase acquisition of nitrogen and phosphorus under stressed and nonstressed conditions. Beneficial microorganisms can also affect the physiological and molecular events of plants. In this study, we discuss how beneficial microorganisms contribute to salt stress tolerance through physiological and molecular events in plants and how those mechanisms work.

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Table Olives as Sources of Bioactive Compounds

Dimitrios Boskou , ... Maria Lisa Clodoveo , in Olive and Olive Oil Bioactive Constituents, 2015

Combining Tradition and Innovation to Improve Nutritional Value of Table Olives

Probiotic food products contain beneficial microorganisms large enough to reach the intestine and exert an equilibrating action on the intestinal microflora, reducing the amount of pathogens and helping boost the immune system, thus lowering the risk of gastrointestinal diseases. In the past two decades, probiotic health-promoting microorganisms have been included in commercial products as a response to the consumer demand for healthy foods that improve overall health, intestinal function, and digestion. Fermented foods, such as table olives, can be reinforced with probiotic bacteria and can be used as a vehicle for incorporating probiotic cultures. The incorporation of health-promoting bacteria into table olives would add functional features to their current nutritional properties ( Arroyo-López et al., 2012; De Bellis et al., 2010; Gomez et al., 2014; Lavermicocca et al., 2005; Rodriguez-Gómez et al., 2013, 2014). Pure starter cultures of lactic bacteria are available in the market and used in several vegetable fermentations (Leroy and De Vuyst, 2004), but their use in table olive processing is still limited. A probiotic potential is expected to greatly enhance the already important nutritional value of table olives and convey a favorable economic impact.

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Microbial-based inoculants in sustainable agriculture: Current perspectives and future prospects

Ajinath Dukare , ... Vikas Sharma , in Biofertilizers, 2021

13.3 Important functional groups and plant growth promotion aspects of microbial inoculants

Plant growth-promoting beneficial microorganisms (PGPMs), referred to as microbial inoculants, are the potential components for resolving the agroecological problems, as they are capable of boosting plant health through growth promotion, enhanced nutrient acquisition, and disease suppression ( Adesemoye and Kloepper, 2009). Microbial inoculants exploited in agriculture comprise the following main groups: (1) PGPRs, (2) arbuscular mycorrhizal fungi (AMF), and (3) the nitrogen-fixing rhizobia. The rhizosphere inhabiting beneficial microorganisms such as bacteria, fungi, and algae are exploited for achieving the desired goals of sustainability (Vejan et al., 2016). Plant growth promotion using these microbial inoculants is successful due to their ability of: (a) effective root colonization and competency, (b) rapid multiplication, (c) adaptation to a diverse and extreme soil ecosystem, and (d) exploitation of diverse compounds as a source of nutrition. Among them, PGPRs are more efficient in rhizosphere colonization and plant growth support, following inoculation onto the surface of seeds. Besides this, they can also colonize the root surface (rhizoplane) and within radicular tissues (the root itself) (Gray and Smith, 2005). Presently, the use of PGPRs for the revival of soil and plant health and, thereby, increased agricultural productivity has been explored in several parts of the globe.

Plant-soil associated microenvironments, particularly the rhizosphere and rhizoplane, are occupied in great abundances by useful microbes. These microbiota, often involved in antagonistic and mutualism interactions, ensure augmented plant growth and yield (Bhardwaj et al., 2014). As depicted in Fig. 13.1, probable plant-microbes interactions and interconnected signaling among them occur in the crop rhizosphere and are implicated in the stimulation of plant growth, biological suppression of harmful pathogens, and mitigation of crop abiotic stresses through multifold mechanisms of beneficial rhizosphere microbiota. The positive effects of rhizobacteria on plant growth and soil health are exerted via the mechanism of nitrogen fixation, solubilization, and supply of plant nutrients, hormonal stimulation, improving root growth, and enhanced uptake of nutrients and water (Meena et al., 2017a; Gouda et al., 2018). In addition, they indirectly enhance crop growth by inhibiting activities of plant-associated harmful fungi through antibiosis, myco-parasitism, detoxification of pathogen virulence, competitive exclusion of nutrients, and stimulation of plant defense (Tripathi et al., 2012).

Fig. 13.1

Fig. 13.1. Schematic representation depicting the probable plant-microbes interactions occurring in the crop rhizosphere and implicated in the stimulation of plant growth, biological suppression of harmful pathogens, and mitigation of crops abiotic stresses through multifold mechanisms of beneficial rhizosphere microbiota. In plant microbe interactions, numbers of cellular chemicals are involved which can act as signaling molecules for the activation and regulation of gene and enzyme functions in both beneficial microorganisms and the plant system. Abbreviations: AHL, N-acyl homoserine lactones; MAMPs, microbe-associated molecular patterns; QSM, quorum sensing molecules; SA, salicylic acid; VOCs, volatile organic compounds.

 (Modified from Gouda, S., Kerry, R.G., Das, G., Paramithiotis, S., Shin, H.S., Patra, J.K., 2018. Revitalization of plant growth promoting rhizobacteria for sustainable development in agriculture. Microbiol. Res. 206, 131–140.)

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Mycorrhizal Association and ROS in Plants

Qiang-Sheng Wu , ... Elsayed Fathi Abd-Allah , in Oxidative Damage to Plants, 2014

Plant rhizosphere usually inhabits beneficial microorganisms distributed in the soil ecosystem, namely, arbuscular mycorrhizal fungi. The helpful fungi can form mycorrhizal associations with the plant roots, which help the host to uptake nutrient elements and water from the soils. ROS within plants is a very interesting field of research. ROS generated in the cell has negative impact on biomolecules and in severe case causes death of the cell. Relations between the mycorrhizal associations and ROS are widely concerned with plants. Mycorrhizal symbiosis generally restricts the oxidative burst under environmental stresses. As a result, arbuscule is associated with accumulation of H 2O2, and more accumulation of H2O2 in arbuscules may predict the collapse or degradation of arbuscules during the mycorrhizal development. On the other hand, mycorrhizal association can enhance antioxidant enzyme activities and increase antioxidant contents of the host plant, thus partly alleviating oxidative stress. The mycorrhiza-mediated antioxidant defense systems may be dependent on both growth conditions and tissues of the host plant. Interestingly, arbuscular mycorrhizas themselves possessed various SOD genes to up-regulate stress tolerance, whereas the mycorrhizal mediation is fully known. In this chapter, we simply introduced mycorrhizal symbiosis, summarized the ROS occurrence under mycorrhizal symbiosis, and also clarified the roles of mycorrhizal association in antioxidant enzymes and antioxidants of the host plant. Relation of arbuscular mycorrhizas with ROS in plants in future is also discussed.

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Overview and challenges in the implementation of plant beneficial microbes

Vivek Sharma , ... Richa Salwan , in Molecular Aspects of Plant Beneficial Microbes in Agriculture, 2020

1.3 Plant microbiome and its potential

The marketing of plant beneficial microorganisms are of vital significance in agricultural fields due to their environmental safety, sustainability and multiple benefits to the host plants as discussed earlier for better nutrients acquisition, enhanced plant growth and tolerance to environmental stress factors ( Sharma et al., 2017a,b). The plant associated microbiome, gained the attention, due to tie multiple benefits to the host plants. The plant microbiome comprises the different useful gene pool of prokaryotic and eukaryotic origin which is linked with the habitats of host plant. The microbiome in plant rhizosphere works as extremely evolved exterior active milieu for plants (For more detail information see Bais et al., 2006; Badri et al., 2009; Pineda et al., 2010; Philippot et al., 2013; Rout and Southworth, 2013; Spence et al., 2014). In other words, it represents the second genome of the plant (Berendsen et al., 2012) and reveal positive or negative effect on plant productivity, immunity and yield (Lakshmanan et al., 2014). The co-inoculation of PGPR or AMF, found to enhance the efficient use of fertilizers. For example, the combined use of PGPR and AMF was found, better suited to for N and P uptake compared to fertilizers alone (Adesemoye et al., 2009). Different plant beneficial microorganisms such as Azotobacter, Azospirillum, Bacillus spp, Pseudomonas, Rhizobium, blue green algae and other PGPRs, deliver substantial quantity of N for the plant growth and crop productivity (Choudhury and Kennedy, 2004; Dhanasekar and Dhandapani, 2012; Bhardwaj et al., 2014).

The inoculation of Rhizobium trifolii in Trifolium alexandrinum plants, led to high number of nodulation and higher biomass under saline stress (Hussain et al., 2002; Antoun and Prevost, 2005). Similar to this, the inoculation of P. fluorescens MSP-393, led to the production of osmolytes and salt-stress induced proteins which help the plants under salinity (Paul and Nair, 2008). Also, the inoculation of P. putida Rs-198 strain enhanced seed germination and plant growth under high salt and alkaline conditions by upregulating the transport of K+, Ca2+ and Mg2+ and by declining the Na+ absorption (Yao et al., 2010). In a few cases, Pseudomonas strains also imparted systemic response in Arabidopsis thaliana against P. syringae by 2,4-diacetylphloroglucinol (DAPG) (Schnider-Keel et al., 2000; Weller et al., 2012). The production of calcisol via P. alcaligenes PsA15 and Bacillus polymyxa, imparts tolerance abiotic stresses such as high temperature and saline conditions (Egamberdiyeva, 2007). The inoculation of AM fungi also increases plant growth under saline conditions. In other case, inoculation of Achromobacter piechaudii strains enhances the tomato and pepper plants biomass under water stress and NaCl concentration level of 172   mM (Alavi et al., 2013). The root endosymbiont fungi Piriformospora indica, induced defense response in host plants against saline stress. Moreover, Azotobacter in addition to nitrogen fixation, secreted thiamine and riboflavin, plant growth regulators Including IAA, gibberellin (GA) and cytokinin.

The arbuscular mycorrhizal fungi belonging to the subphylum Glomeromycotina, are obligate symbionts in more than >60% of terrestrial plant species (van der Heijden et al., 2015; Spatafora et al., 2016). These fungi play vital role in the nutrients acquisition (Smith and Read, 2008), enhancing the resistance to pathogens (Vigo et al., 2000) and/or tolerance to water scarcity and osmotic stress in the associated host plants (Augé et al., 2015). The mycelia of mycorrhizal member acquire ammonium and nitrate from nearby soil and then afterward, these molecules are obtained by mantle and hartig net, from there they are supplied to the associated plant. The mycorrhiza orchestrated N uptake is predominant in organic agricultural fields or under drought (Hodge and Storer, 2015; Bukovská et al., 2018; Řezáčová et al., 2018a,b). In exchange of N and P, the fungus receive food in the form of simple carbohydrates and/or fatty acids (Roth and Paszkowski, 2017) and its amount varies from 0.9 to 20%, of host plant gross photosynthesis rate (Konvalinková et al., 2017; Slavíková et al., 2017). However, the precise mechanism responsible for nutrient flow, still not precisely discovered (Bücking et al., 2016).

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