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1 Introduction

Fluorescent Pseudomonas had always played an important role in the development of biopesticides and biofertilizers since the concern for more sustainable agricultural production systems exists. A huge background regarding the application of these microorganisms for plant fertility purposes can be traced to the first patent obtained in the 1910s (Coates 1910). Since that, fluorescent Pseudomonas have gained more and more relevance, and nowadays they can be compared to rhizobia in terms of scientific knowledge and applied research.

Fluorescent Pseudomonas are a heterogeneous collection of non-enteric strains, Gram-negative chemoheterotrophs, and generally aerobic, non-fermentative, and mobile bacteria which have a polar flagellum (Dwivedi and Johri 2003). The genus is comprised of the species P. aeruginosa, P. aureofaciens, P. chlororaphis, P. fluorescens, P. putida, and more recently P. protegens and also plant-pathogenic species such as P. cichorii and P. syringae. Fluorescent Pseudomonas differ from other Pseudomonas spp. for their distinctive soluble yellowish-green pigment, which corresponds to the siderophore called pyoverdin, which emits light when exposed to ultraviolet radiation (Meyer and Abdallah 1978). What makes pseudomonads so interesting? It is because of the fact that they have excellent root-colonizing ability and a wide battery of mechanisms to promote plant growth (i) directly by facilitating nutrient acquisition or synthesizing phytohormones and (ii) indirectly by biological control of plant pathogens. Besides, they are very suitable for being applied as inoculants; for instance, they can use a variety of carbon sources, are amenable to genetic manipulation, are abundant in soil and roots, have a high growth rate, and can be introduced into the rhizosphere by seed bacterization (Whipps 2001).

Fluorescent Pseudomonas have been applied successfully to control plant pathogens on different pathosystems, and as the interest of reducing chemical pesticide inputs on different crops increases, the number of host plant increases too. Biocontrol mechanisms are diverse and can be simultaneously exerted by a single strain or a combination of strains. The main mechanisms involve the synthesis of secondary metabolites like antibiotics, the induction of systemic resistance in the host plant, and the competition for niches and nutrients.

Direct promotion of plant growth mediated by fluorescent Pseudomonas is another approach to reduce the use of chemical fertilizers. Fluorescent Pseudomonas exert this effect by improving plant nutritional status and/or by synthesizing plant hormone-like compounds.

2 Mechanisms that Promote Plant Health by Fluorescent Pseudomonas spp.

2.1 Antibiotics: Diversity of Antimicrobial Metabolites Produced by Pseudomonas spp.

Early studies on suppression of plant pathogens by antagonistic bacteria were focused on their ability to produce siderophores which efficiently compete for iron acquisition, so that pathogens remain devoid of this nutrient (Kloepper et al. 1980). However, in the last 30 years, it was demonstrated that other secondary metabolites such as antibiotics, enzymes and volatile compounds have an important role in controlling pathogen development (Weller 2007; De La Fuente et al. 2004).

Most fluorescent Pseudomonas strains are capable of synthesizing one or more antibiotics (Weller 2007). The structure, biosynthetic pathways and regulation of the main antibiotics produced by Pseudomonas spp. have been fully characterized. Among them are the phenazine derivatives, 2,4-diacetylphloroglucinol, pyrrolnitrin, pyoluteorin and cyclic lipopeptides.

Phenazines are heterocyclic nitrogen-containing secondary metabolites, produced not only by Pseudomonas but also by various microbial genera like Brevibacterium, Burkholderia and Streptomyces, among others (Mavrodi et al. 2006). It has been described over 100 phenazine derivatives of microbial origin, and a single microorganism can produce up to ten of these ones (Dwivedi and Johri 2003; Mavrodi et al. 2013). Phenazine compounds have a broad spectrum of activity against bacteria, fungi, and parasites. Their mode of action relies on its redox properties and the capacity to promote the production of toxic reactive oxygen species (ROS) in the target organism (Mavrodi et al. 2012). However, their biocontrol activity has also been attributed to the induction of systemic resistance (ISR) in the host plant and the reduction in toxin production by the pathogen. For instance, phenazine 1-carboxylic acid (PCA)-producing Pseudomonas fluorescens LBUM223 controls the development of common scab in potato caused by Streptomyces scabies. But the antagonistic effect was demonstrated not to be mediated by antibiosis but, instead, by a reduction in the expression of thaxtomin A by S. scabies which is necessary to produce the necrotic lesions or scabs. In field trials, an increase of 46 % in tuber weight was achieved by inoculation with LBUM223, which did not reduce pathogen soil populations, but altered the expression of a key pathogenesis gene, leading to reduced virulence (Arseneault et al. 2013, 2015).

Five enzymes are required to transform the chorismate in pyocyanin (PYO) or phenazine-1,6-dicarboxylic acid (PDC), which are encoded by a gene cluster that also contains genes involved in regulation, transport, resistance and transformation of PYO/PDC to strain-specific phenazine derivatives (Mavrodi et al. 2013). Several studies have demonstrated that phenazines are involved in the control of soilborne fungal pathogens. It was shown that some indigenous PCA-producing Pseudomonas strains could locally reach high concentrations of the antibiotic around the roots, estimated over 100 mM, enough to inhibit Rhizoctonia solani AG-8, an important pathogen of wheat (Mavrodi et al. 2012). The phenazines produced by Pseudomonas spp. are also able to inhibit pathogens such as F. oxysporum, Pythium spp., Gibberella avenacea, Alternaria spp. and Drechslera graminea (Mavrodi et al. 2006).

The antimicrobial metabolite 2,4-diacetylphloroglucinol (DAPG) is another example of a widely characterized antibiotic produced by fluorescent Pseudomonas spp. This polyketide compound is responsible for suppressiveness of plant diseases such as tobacco black root rot (Keel et al. 1996) and wheat take-all (Raaijmakers and Weller 1998). DAPG spectrum of action is quite broad and covers bacteria, fungi, oomycetes and nematodes. Recent studies in Saccharomyces cerevisiae provided evidence of the mode of action of DAPG. This compound acts as a proton ionophore interrupting the proton gradient in the mitochondrial membrane, which explains their broad spectrum of action in various eukaryotes (Gleeson et al. 2010; Troppens et al. 2013). The biosynthetic locus involved in the antibiotic production includes phlA, phlC, phlB and phlD, responsible for the production of monoacetylphloroglucinol (MAPG) and its conversion to 2,4-DAPG, together with genes encoding efflux and repressor proteins (Bangera and Thomashow 1996; Bangera and Thomashow 1999).

Pyrrolnitrin and pyoluteorin are also extensively characterized antibiotics. The first is a chlorinated phenylpyrrole which is synthesized from L-tryptophan and whose mode of action involves the inhibition of the respiratory chain in fungus. Given its strong antifungal activity, it has been used to develop topical antimycotics for human use or even fungicides for agricultural application (Gross and Loper 2009). The biosynthetic gene cluster involved in pyrrolnitrin synthesis consists of four highly conserved genes, prnABCD, that encode enzymes responsible for the conversion of L-tryptophan in pyrrolnitrin in P. fluorescens. On the other hand, pyoluteorin is an aromatic polyketide antibiotic that consists in a resorcinol ring attached to a dichlorinated pyrrole moiety. A hybrid nonribosomal peptide synthetase/polyketide synthase (NRPS/PKS) is responsible for pyoluteorin synthesis: the resorcinol ring is synthesized by PKS, while the dichloropyrrol is synthesized from L-proline by NRPS. The biosynthetic operon contains 17 genes, including transport and regulatory genes (Nowak-Thompson et al. 1999). Pyoluteorin is especially toxic to oomycetes and some fungi and bacteria (Howell and Stipanovic 1980), but its mode of action has not yet been clarified.

Fluorescent Pseudomonas spp. can also synthesize volatile antimicrobial compounds whose actions are exerted at greater distances than diffusible antibiotics. Within volatile compounds, hydrogen cyanide (HCN) has been the most studied and it is commonly produced by pseudomonads inhabiting soils (Gross and Loper 2009). HCN is a strong inhibitor of metalloenzymes such as cytochrome oxidase; therefore, it is toxic for most organisms (Blumer and Haas 2000). Its production in the rhizosphere environment has shown to contribute to the control of pathogens. The compound is synthesized from glycine by an HCN synthase complex, which is encoded by three structural genes hcnABC. The operon is highly conserved among cyanogenic Pseudomonas (Loper and Gross 2007), but the genomic context is not conserved, differing among species. The HCN biosynthetic locus had also been reported in Chromobacterium violaceum and several species of Burkholderia. An example of biological control of a plant pathogen mediated by HCN production is by the use of P. fluorescens CHA0 whose ability to produce HCN contributes to the biocontrol of black root rot caused by Thielaviopsis basicola, in tobacco (Voisard et al. 1989). There are reports of Pseudomonas that inhibit the growth of pathogenic fungi by the production of volatile compounds other than HCN. In many cases these compounds were not identified (Fernando et al. 2005; Trivedi et al. 2008; Weisskopf 2013). But, in other cases, the presence of undecene, undecadiene, (benzyloxy)benzonitrile (Kai et al. 2007), nonanal, benzothiazole and 2-ethyl-1-hexanol (Athukorala et al. 2010) was found.

Another group of secondary metabolites widely distributed among the fluorescent Pseudomonas spp. is cyclic lipopeptide (CLP) biosurfactants. These compounds are also produced by Bacillus spp. They are amphipathic compounds with an enormous structural diversity that reflects a broad variety of natural roles, some of which may be unique to the producing microorganism (Raaijmakers et al. 2010). CLP are basically composed of a lipid chain attached to a short oligopeptide (8–25 amino acids) that can be linear or cyclic (Raaijmakers et al. 2006). The peptide moiety is synthesized by NRPS which are able to incorporate non-proteinogenic amino acids such as D-amino acids, β-amino acids and hydroxy- or N-methylated residues (Mootz et al. 2002). These non-proteinogenic amino acids protect the synthesized peptide against the action of ubiquitin-dependent proteases (Hashizume and Nishimura 2008). An initial condensation domain is responsible for the attachment of the lipid moiety to the growing peptide chain, which can be of different length even for the same CLP. These compounds usually show strong lytic and growth-inhibitory activities against a variety of microorganisms including viruses, mycoplasma, bacteria, fungi and oomycetes, giving to the producing microorganisms an important advantage in the competition for niches (Raaijmakers et al. 2010). The proposed mode of action is the disruption of cell membranes by pore formation which triggers an imbalance in transmembrane ion fluxes and cell death (van de Mortel et al. 2009). CLP also have a role in bacterial motility and solubilization and diffusion of substrates. Mutants unable to produce CLP usually show little or no motility, which can be recovered by exogenously addition of CLP (de Bruijn et al. 2007). This function is important for microbial dispersal and colonization of ecological niches. Various strains of Pseudomonas spp. have proven to be more effective in colonization of roots than their mutant strains (Braun et al. 2001; Nielsen et al. 2005; Tran et al. 2007). CLP might also have an important role in adhesion to surfaces and biofilm formation that depends on the structure of the CPL. Some mutant strains of Pseudomonas spp., unable to produce CLP, generate unstable biofilm as compared with the wild strain (Roongsawang et al. 2003; Kuiper et al. 2004). In other cases, the absence of CLP caused a significant reduction in biofilm formation (de Bruijn et al. 2007; de Bruijn et al. 2008). Finally, CLP may have a role in the induction of systemic resistance (ISR) in plants. For example, inoculation of tomato plants with a massetolide (CLP)-producing strain or the pure compound increased the plant leaves’ resistance against Phytophthora infestans infection (Tran et al. 2007). It is unknown if specific receptors are needed in host plants, but it is thought that CLP can generate distortions or transient channels in plant membranes, initiating a cascade of responses that leads to an increased expression of the plant defense system (Jourdan et al. 2009).

Successful examples of biological control mediated by antibiotic-producing fluorescent Pseudomonas were described for forage legumes damping-off seedling diseases (De La Fuente et al. 2004; Quagliotto et al. 2009; Yanes et al. 2012). For instance, P. protegens UP61 strain, which can produce HCN, 2,4-diacetylphloroglucinol, pyrrolnitrin and pyoluteorin, can densely colonize the roots of lotus (Lotus corniculatus) and alfalfa (Medicago sativa L.) and is capable of controlling damping-off caused by Pythium spp. on both forage legumes (De La Fuente et al., 2004; Quagliotto et al. 2009). Several strains isolated from alfalfa rhizosphere also demonstrated a significant ability to control seedling diseases caused by Pythium debaryanum and promoted alfalfa growth (Yanes et al. 2012). Among these strains P. fluorescens C119, which produces a CLP with antimicrobial activity, notably promoted the growth of alfalfa (Fig. 15.1).

Fig. 15.1
figure 1

Field assay conducted to determine the biocontrol activity and plant growth-promoting effect of P. fluorescens C119 strain. Alfalfa seeds were coinoculated with the pseudomonad strain and Sinorhizobium meliloti using a peat-based formulation. Coinoculated plants (a) showed a significant increase in alfalfa yield in comparison to the control plants (b) which were inoculated only with S. meliloti. The picture in the bottom shows a partial view of the field assay

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2.2 Biological Control Mediated by Niche and Nutrient Competition

Successful root colonization depends on the ability to compete for nutrients in the root. Competition between beneficial and pathogenic microorganisms by niches in the root surface can result in a decrease in the severity of crop diseases (Kamilova et al. 2005). It is important that beneficial microorganisms colonize efficiently the site of the root that the pathogen uses to get into the plant. Pliego and coworkers (2008) isolated the strains Pseudomonas pseudoalcaligenes AVO110 and P. alcaligenes AVO73, which were selected by their excellent root-colonizing ability in avocado and antagonism against Rosellinia necatrix. Both strains efficiently colonized different sites of the root, but only AVO110, which was located on the same site as the pathogen, demonstrated a significant protection effect against avocado white root rot.

Competition for iron as biological control mechanism has been widely documented. In the soil, iron availability in the soluble form Fe3+ is generally limited. To get access to this nutrient, many microorganisms produce siderophores which are chelant molecules with high affinity for iron. Competition for iron was first reported by Kloepper and colleagues in 1980. Siderophores are structurally diverse and are classified according to their functional group as catechols (enterobactin, vibriobactin, yersiniabactin and pyochelin), hydroxamates (alcaligin and deferoxamine B), and carboxylates (staphyloferrin A and achromobactin) (Miethke and Marahiel 2007). Some Pseudomonas are able to internalize the ferric ion using heterologous siderophores synthesized by cohabiting rhizosphere microorganisms, producing a nutrient deficiency that affects the development of competing microorganisms (Loper and Henkels 1999; Saharan and Nehra 2011). An example of an iron competitor strain is the pseudobactin producer P. putida WCS358 that is capable to control diseases caused by Fusarium spp. in carnation and radish (Weisbeek and Gerrits 1999). The effectiveness of this mechanism was demonstrated by an increase in potato yield when seeds were treated with WCS358 wild-type strain, whereas a siderophore-negative mutant had no effect on tuber yield in field assays (Duijff et al. 1994).

2.3 Induction of Defense Responses in Plants

Some nonpathogenic rhizobacteria interact with host plants stimulating an alertness state that would protect plants against subsequent pathogen attack, a phenomenon known as induction of systemic resistance (ISR). This state of preparation for a possible attack enables a fast triggering of defense responses which spread to every organ of the plant, in the presence of a pathogen. While several molecules synthesized by inducing defense bacteria are known to stimulate ISR, there is little information about the molecular mechanisms involved in plant cell recognition of such elicitors. Bacteria-produced molecules involved in the ISR phenotype are lipopolysaccharide (Leeman et al. 1995), siderophores (Maurhofer et al. 1994), flagella (Meziane et al. 2005), and some antibiotics such as those produced by fluorescent Pseudomonas spp.: 2,4-diacetylphloroglucinol (Weller et al. 2012), pyocyanin (Audenaert et al. 2002), biosurfactants (Ongena and Jacques 2008), and volatile organic compounds (Ryu et al. 2004). Given this wide variety of elicitors and the enormous diversity of microorganisms that inhabit the rhizosphere, we would expect that plants stand in a continuous state of alert. However, field studies have determined that an effective ISR requires a population density of at least 107 CFU of the inducing bacteria per gram of root. For Pseudomonas spp., a dose-response study has shown that there is a threshold of 105 CFU per gram of root to trigger ISR responses (Raaijmakers et al. 1995). As it is very unlikely to find such a population density of a specific bacterial genotype on a rhizospheric soil, thus it is very unlikely to find a natural phenomenon of ISR in a soil, except in a suppressive soil (Bakker et al. 2013).

3 Mechanisms Involved in Plant Growth Improvement by Rhizospheric Pseudomonas spp.

3.1 Nutrient Contribution to the Host Plant

Some bacteria including fluorescent Pseudomonas spp. can promote plant growth by two major mechanisms: assisting plant nutrition by solubilization of soil nutrients and/or contributing to the pool of the host plant’s growth hormones.

Microorganisms that produce metabolites or enzymes that increase the bioavailability of essential plant nutrients such as nitrogen, phosphorus and iron are called biofertilizers (Glick et al. 2007; Berg 2009). The supply of nitrogen by atmospheric N2-fixing bacteria is the most widely studied example of biofertilization. These bacteria can be endosymbionts, as rhizobia, or free-living diazotrophs that colonize plant rhizosphere, as Azospirillum. They synthesize an enzyme complex called nitrogenase which catalyzes, by an energetically costly process, the reduction of N2 to ammonia; then, the ammonia is taken up by the plant for the biosynthesis of N compounds. Both plants and microorganisms are benefited, because the plants in turn provide carbonated compounds (photosynthates) to the symbiont (Berg 2009). Until a few years ago, it was thought that the genus Pseudomonas did not perform atmospheric nitrogen fixation. However, after sequencing the entire genome of Pseudomonas stutzeri A1501, it was found that the strain has all the genes necessary to fix N2, organized in a genomic island possibly obtained by horizontal gene transfer (Yan et al. 2008). This genomic region of P. stutzeri A1501 was used to transform P. protegens Pf-5 strain, an excellent biocontrol agent of plant diseases. The transformed strain was able to promote the growth of Arabidopsis thaliana and other plants of agronomic interest such as alfalfa, fescue and corn under conditions of nitrogen deficiency, opening a new perspective for the production of genetically modified inoculants (Setten et al. 2013).

Phosphorus is an important nutrient and the second limiting element of plant growth, after nitrogen (Gyaneshwar et al. 2002). Phosphate-solubilizing bacteria are another example of biofertilizers, which are taking great relevance due to the high agronomic demand for this nutrient. Most agricultural soils have large reserves of phosphorus due to the repeated application of chemical fertilizers. However, phosphates react with numerous ionic components of the soil, being rapidly immobilized in organic forms by metabolic reactions or in soil mineral particles by adsorption and precipitation. These forms of phosphate are not bioavailable to plants, and only a small fraction of these phosphate forms are available for root absorption (Gyaneshwar et al. 2002). Between 30 and 70 % of the phosphorus in the soil is in organic forms (Shang et al. 1996). Soil microorganisms play an important role in the phosphorus cycle as they produce molecules that assist phosphorus assimilation by plants (Richardson and Simpson 2011). Two processes are involved in the mobilization of phosphates by soil microorganisms: mineralization of organic phosphorus and solubilization of phosphorus from inorganic sources. Various enzymes such as nonspecific phosphatases, phytases, phosphonatases and C-P lyases release the phosphorus from the organic fraction, while the inorganic phosphorous is mainly released by organic acids such as gluconic acid (Berg 2009; Werra et al. 2009). In summary, phosphate-solubilizing bacteria (PSB) can increase the phosphorus content in plant tissues (Awasthi et al. 2011). Among the best-known PSB are species belonging to the genera Pseudomonas, Bacillus, Paenibacillus, Escherichia, Acinetobacter, Enterobacter and Burkholderia (Collavino et al. 2010).

3.2 Plant Growth Promotion Mediated by Microbial Phytohormone Production

Plant hormones govern plant growth by spatial and temporal control of division, growth and differentiation of cells. Phytohormones also play an essential role in responses to biotic and abiotic stresses (Peleg and Blumwald 2011). Microorganisms that produce phytohormone-like compounds contribute to the pool of hormones produced by the host plant, intervening in the physiology and promoting plant survival (Dodd et al. 2010; Morel and Castro-Sowinski 2013). Phytohormones act at low concentrations and can be classified in three types: auxins, cytokinins and gibberellins. Indole-3-acetic acid (IAA) is the most commonly found auxin among rhizobacteria. There are at least five biosynthetic pathways for the synthesis of IAA, which mostly use tryptophan (Trp) as precursor. The presence of IAA in the rhizosphere stimulates the formation of lateral roots and root hairs, which greatly increases the absorption surface of roots (Duca et al. 2014). Plants that produce root exudates rich in tryptophan are more prone to be affected by IAA-producing bacteria than those that do not excrete this amino acid precursor. For example, a growth-promoting effect was observed in radish plants, which excrete large amounts of Trp, when inoculated with the IAA-producing strain P. fluorescens WCS365, while no effect was observed in plants that excrete tenfold less Trp like tomato, cucumber and pepper (Kamilova et al. 2006).

Cytokinins are involved in cell division and have effects on roots, leaves, flowers, fruits and seeds. The apex of the roots and germinating seeds contains high concentration of cytokinins (Pliego et al. 2011). Members of the genera Pseudomonas, Agrobacterium, Erwinia, Paenibacillus, Azotobacter, Azospirillum, Bacillus and Rhizobium are cytokinin-producing bacteria, which are also capable of promoting plant growth (García de Salamone et al. 2001).

Gibberellins are involved in various physiological processes of higher plants, in especial root elongation (Pliego et al. 2011). There are more than 130 known gibberellins, which are diterpenoids synthesized by fungi and bacteria (Dodd et al. 2010). The first report of a bacterial gibberellin biosynthetic pathway was for a strain of B. japonicum (Morrone et al. 2009). Kang and coworkers (2014) demonstrated that the gibberellin-producing strain P. putida H-2-3 provides the hormone to gibberellin biosynthesis-deficient mutant Waito-C rice plants and also enhances the growth of soybean under saline or drought stresses.

Some bacteria, including Pseudomonas spp., are able to decrease the formation of ethylene by plants through the production of the enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase. The enzyme hydrolyzes ACC, a precursor of ethylene synthesis, with the formation of α-ketobutyrate and ammonium. Plants produce ethylene in response to environmental stresses (Penrose et al. 2001). In these situations plants produce two pulses of ethylene: a small pulse a few hours after the sustained stress is imposed, which is likely to activate the defense genes, and a second pulse of production, a more intense one a few days later. This second pulse of ethylene production generates negative effects on the plant such as senescence, abscission and chlorosis (Glick et al. 2007). It has been proposed a model that explains the promoting effect of ACC deaminase-producing bacteria (Glick et al. 2007) as follows: IAA-producing bacteria can stimulate the synthesis of ACC synthase in plants, which converts S-adenosyl methionine (SAM) in ACC. The ACC is partly exuded by the roots where it is hydrolyzed by ACC deaminase-producing bacteria. To maintain the balance between the concentrations of ACC in and out of the roots, the plant secretes more ACC, decreasing the amount of available ACC necessary to produce ethylene and thus reducing the inhibition effect imposed by ethylene in a stressful situation. The repression of IAA synthesis mediated by ethylene also decreases which results in an increased production of this hormone, increasing the promoting effect. Genes for synthesis of ACC deaminase have been characterized in several strains of Pseudomonas spp. (Klee et al. 1991; Cheng et al. 2007), and many of them had proved to be involved in the phenotype of plant growth promotion under stress conditions. For instance, Zahir and colleagues (2011) reported a significant improvement of root elongation, nodulation, and yield of lentil when plants were coinoculated with ACC deaminase-producing Pseudomonas jessenii and Rhizobium leguminosarum in pot assays and field trial. They showed the implication of ACC deaminase-producing bacteria in the recovery of stressed lentil plants by a bioassay that involved the addition of 6 mM ACC to etiolated lentil seedlings. This triggered an ethylene-specific triple response that consisted in a decrease in root length and shoot length and an increase in shoot diameter. Such effect was significantly reduced when seedlings were coinoculated with both rhizobacteria, which were even more effective than the addition of CoCl2, an inhibitor of ethylene production.

4 Fluorescent Pseudomonas into the Market

Fluorescent Pseudomonas have been widely explored as biocontrol agents and biofertilizers due to the several characteristics mentioned above. However, compared to the volume of research that has been performed with these bacteria, few strains have been successfully developed into commercial products. In Table 15.1, a list of Pseudomonas-based products for plant biocontrol and biostimulation has been reviewed.

Table 15.1 Pseudomonas spp.-based commercial products for biocontrol or biofertilization, formulated alone or in combination with other PGP microorganisms
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A successful example is the biocontrol agent Pseudomonas chlororaphis strain MA342, which has been formulated in several commercial products. Initially, MA342 was tested in 105 field experiments in different zones of Sweden for 5 years to control seed-borne diseases of barley, oats, wheat and rye. After consistent results, comparable to chemical fungicide application, an inoculant formulation was developed for the protection of cereals and then for peas. However, the performance of these microorganisms may not always be consistent, as showed by their high effectiveness against Alternaria spp. on cabbage and carrots and against Colletotrichum lindemuthianum on beans, but a poor performance in seed-borne Ascochyta spp. on peas (Amein et al. 2011; Johnsson et al. 1998; Tinivella et al. 2009). Thus, all plant-pathogen interactions can not be overcome by the inoculation with a single Pseudomonas strain.

5 Benefits and Challenges of Using Fluorescent Pseudomonas for Plant Growth Promotion

The application of beneficial microorganisms to improve plant health of economically important crops has many advantages over chemically synthesized pesticides and fertilizers as they are safer with the environment, have a specific targeted activity, do not favor the development of resistant pathogens due to the diversity of mechanisms involved in their biocontrol phenotype, are effective in small doses, decay faster, and can be applied either in conventional or integrated management systems (Berg 2009). Fluorescent Pseudomonas are a good example of the sustainable use of microbes, but the commercial adoption of agricultural products based on these bacteria is not so widespread, due to some drawbacks that their application still present and that need to be overcome.

5.1 Consistency in Field Performance

As also happens with other plant growth-promoting rhizobacteria (PGPR) (except from rhizobia and some free-living nitrogen fixers), the lack of consistency in field performance of Pseudomonas-based bioproducts, in different crops and conditions, is a limitation for its commercial application (Barreto et al. 2010). In some cases, there is a gap between results obtained in controlled laboratory conditions and those achieved in the field. Different host-plant genotypes produce root exudates with different chemical compositions. These variations may play a role in the bacterial responses, which are needed to support inoculum presence and activity (Khalid et al. 2004; Dalmastri et al. 1999). Usually, the process of plant breeding for the selection of cultivars does not take into account the association of plant with beneficial microorganisms. Considering this aspect, it would be a valuable tool to coordinate the selection of host plant varieties and biofertilizers; this strategy could enhance the ability of the microorganism to interact with the plant and to express promotion traits, e.g., production and responsiveness to hormones (Remans et al. 2008).

The failure of microorganism-based protectant formulations under field conditions has been explained by their low stability, with limited persistence and resistance, but not by a lack of effectiveness (Dorn et al. 2007). This phenomenon can be sometimes explained by the complex regulation of biocontrol-related traits as colonization and production of active metabolites, which are highly dependent on environmental conditions. In some cases, the need for the inoculation with a high population of the biocontrol agent, in order to achieve effective control of the pathogen, is also a limiting factor.

Usually, successful field inoculation experiments have been difficult to establish due to the low disease incidence of plant pathogens during the assays. The strain P. chlororaphis R47 was highly active in the protection of potato against Phytophthora infestans in vitro and in greenhouse, but its activity could not be verified in the field due to unfavorable infection conditions (Guyer et al. 2015). In another study, from 20 field trials installed in two different regions of Uruguay, and during a 4-year evaluation of effectiveness of three P. fluorescens strains to protect alfalfa from emergence diseases, only 11 trials were conducive for damping-off (Quagliotto et al. 2009).

The challenges to overcome this limitation for a wider adoption of Pseudomonas spp. as biofertilizers include the characterization of the ecology and colonization behavior of these bacteria in the rhizosphere at different situations, as well as their mechanisms of plant promotion and regulation. The development of more stable formulations will enable the strains to be established at adequate cell densities in order to behave as plant promoters under field conditions. A comprehensive consideration of the biology and ecology of the crop system, and the agricultural practices, will help to reduce the variation of results in field performance of these inoculant bioformulations (Barreto et al. 2010; Guyer et al. 2015).

5.2 Is Genetic Modification an Option?

Some researchers have proposed the development of genetically modified (GM) microorganisms aimed to combine different plant growth-promoting abilities in a single microbe. For example, the introduction of a plasmid carrying the genomic information for IAA production into P. fluorescens BSP53a, a strain that has the ability to block the development of some phytopathogenic fungi due to siderophore synthesis, was seen as an interesting inoculant strain, which combines plant stimulation and protection effects. The recombinant strain produced an increase in root weight and changes in root morphology, as compared to the wild-type strain in black currant, but not in cherry plants (Dubeikovsky et al. 1993).

Several studies have incorporated antimicrobial traits in Pseudomonas spp strains. When their impact on resident microbial communities was analyzed, the effect caused by inoculation was transient, suggesting a rapid inactivation of the antibiotic in the soil (Bajsa et al. 2013). However, a long-term effect in wheat rhizosphere was caused by P. putida strains that constitutively express PCA or DAPG, which changed the resident bacterial communities in a 4-year experiment (Viebahn et al. 2006).

This approach, the use of GM microorganisms, is a matter of serious controversy in terms of the spread of a GM bacterium in nature, especially if the microbe has better colonization, competence, or persistent abilities in the natural environment. The constraints for the registration of natural microbes for their application in the environment are numerous, but even more are with GM strains that would involve a more detailed risk assessment.

5.3 Let’s Cooperate: Coinoculation

Another strategy to enhance effectiveness and reduce variation in performance is the use of bioproducts with a Pseudomonas strain in combination with another microorganism, presenting additive or synergistic effects, such as nitrogen-fixing bacteria, mycorrhizal fungi, or other plant biocontrol agents. The rhizosphere is a complex ecosystem, as are the interactions involved in plant growth stimulation or disease, so the use of bioformulations containing several PGPR can improve their effectiveness, as compared with single bacterial inoculation (Barreto et al. 2010; Morel and Castro-Sowinski 2013).

Nitrogen-fixing bacteria are widespread PGPR used to improve crop yield, and the nitrogen fertilization using chemicals could be completely prevented if the right strain and adequate management practices are employed. The combination of diazotrophs with other PGPR strain has been widely reported. The coinoculation practice, using Pseudomonas spp. and Rhizobium spp., was demonstrated to enhance nodulation, nitrogen fixation, plant biomass and grain yield in various leguminous species including alfalfa, soybean, green gram, and chickpea. For example, the nodule occupancy by a Rhizobium strain in pigeon pea increased from 50 % to 85 % in the presence of Pseudomonas putida, improving plant growth and nitrogen fixation (Tilak et al. 2006; Remans et al. 2007). In addition,in vitro and in-field experiments carried on in lotus and alfalfa plants showed that the coinoculation with rhizobia and fluorescent Pseudomonas decreases damping-off incidence and fixes nitrogen, compared with single inoculation (Quagliotto et al. 2009; De La Fuente et al. 2002).

The success of this mixed formulation depends also on abiotic factors as nutrient availability, as showed by the following examples. ACC deaminase-producing P. putida UW4 is able to enhance nodulation by Rhizobium in Phaseolus vulgaris mainly under P-deficiency conditions. In this stress situation, the production of ethylene is increased and bacterial ACC deaminase activity can reduce this stress response and revert nodulation inhibition (Remans et al. 2007). ACC deaminase-producing Pseudomonas sp. also promotes groundnut (Arachis hypogea) nodulation by Bradyrhizobium under saline stress condition (Saravanakumar and Samiyappan 2007).

Some bacteria, including strains of Pseudomonas spp., can act as mycorrhiza helper bacteria (MHB), assisting the establishment or promoting the functioning of arbuscular or ectomycorrhizal symbiosis. They can mobilize nutrients from soil, fix nitrogen and protect plant from pathogens, which can lead to enhance fungal germination and root colonization (Frey-Klett et al. 2007; Velivelli et al. 2015). A few examples include the increased infection by ectomycorrhizal fungi as Laccaria spp. and Pisolithus alba in Douglas fir, Eucalyptus and Acacia trees, higher colonization by endomycorrhizal fungi Glomus spp. in diverse plant species (maize, potato, tomato, wheat, barley, clover and Acacia sp.), and protection of papaya from Fusarium oxysporum infection by coinoculation with Pseudomonas spp. and Glomus spp. (Frey-Klett et al. 2007; Hernández-Montiel et al. 2013). The molecular mechanisms involved in these tripartite interactions are poorly understood. For the establishment of the bacteria/mycorrhizal fungus/plant network, the release of active biomolecules and physical contact among the partners seem important, where quorum sensing, biofilm formation and secretion systems seem to be involved (Bonfante and Anca 2009). For instance, ACC deaminase and ethylene production by P. putida is involved in the promotion of endomycorrization by Gigaspora rosea in cucumber (Gamalero et al. 2008). Carbon sources may also be involved in the selection of bacterial communities associated with the mycorrhizosphere. The secretion of trehalose, the main carbohydrate used as carbon sink by the fungus, acts in facilitating the colonization of MH Pseudomonas and formation of biofilms on hyphae (Duponnois and Kisa 2006; Uroz et al. 2007).

Several Pseudomonas strains showed positive effects on the growth of the ectomycorrhizal fungus Laccaria bicolor and the effectiveness of the symbiosis with Populus deltoides roots. Results suggest that these effects are due to the induction of the presymbiotic status of the fungus (Labbé et al. 2014). In other types of interactions, the production of antibiotics by the MHB is stimulated by the mycorrhiza, but this mechanism has not been described yet in interactions with Pseudomonas spp. (Riedlinger et al. 2006).

Plant protection can also be enhanced by the combination of Pseudomonas strains with other protective microorganisms. The coinoculation of faba bean (Vicia faba) with Pseudomonas fluorescens and Rhizobium leguminosarum reduced the symptoms produced by yellow mosaic virus, probably by the induction of the systemic resistance of the plant. Among other examples, the coinoculation of cucumber with Pseudomonas putida and Serratia marcescens and the coinoculation of cucumber and Arabidopsis thaliana with Trichoderma harzianum and Pseudomonas sp. showed additive and positive effects on plants infected with Fusarium wilt (Mohr et al. 2008; Liu et al. 1995; Elbadry et al. 2006; Alizadeh et al. 2013).

5.4 Suitable Formulations for Pseudomonas Delivery

For the successful application of a bioproduct, the formulation (a mixture of ingredients prepared for the direct application on the field or seeds) must deliver the microbial agent in a physiologically active state and with the potential to express all the microbial capabilities (Barreto et al. 2010). Moreover, the product has to be long lasting for a certain period of time to ensure the proper microbial state for effective field application. As Pseudomonas spp. are bacteria that do not produce resistant structures as spores, refrigeration for preservation of the inoculants may be necessary. Temperatures of 4–10 °C enable the conservation of some formulations up to 2–6 months, at room temperature about 3 weeks, but freeze conditions are needed for longer periods. Certain products are marketed as powder-soluble formulas containing lyophilized bacteria and compounds (e.g., milk or canola oil) that improve cell survival and/or effectiveness (Bettiol et al. 2012).

On the other hand, the bacterization of seeds (pre-inoculation of seeds) is also an adequate option of product marketing due to the long-lasting useful life of inoculated seeds that can be stored for long periods (1–2 years) without losing the promoting activity, as it has been shown for P. chlororaphis-based products (Johnsson et al. 1998; Bettiol et al. 2012).

Sterile peat is a carrier that has been extensively used for rhizobial formulations, because it allows bacterial survival during storage and commercialization of the final product. It was demonstrated that this carrier is also suitable for fluorescent Pseudomonas, maintaining constant populations of 10x109 UFC per gram of peat at 4 °C during 6 months (Bagnasco et al. 1998; Date 2001).

5.5 The Tougher Step: Registration

During the process of registration of market products containing microorganisms, and especially when they are based on Pseudomonas spp., a large number of constraints are found (Mathre et al. 1999). A risk assessment to human health and to the environment is needed before releasing a product (Fravel 2005). Bacteria of the genus Pseudomonas include a few species and strains that can be opportunistic human pathogens, so the massive use of formulations containing this microbe is always under debate. Bacteria unable to grow at human body temperature could circumvent this concern, but forward studies are needed to clearly differentiate truly health threat bacteria and safe ones (Bodilis et al. 2004).

As more information regarding safety of microbial formulation is generated, the big challenge may be the simplification of registration procedures, as it occurs with chemical products whose registration is much more standardized despite its potential but known toxicity.

The ecological impact of some Pseudomonas strains is expected to be low, as their populations rapidly decrease after been inoculated, in 1–2 weeks or months in field or greenhouse conditions. This could be a favorable trait for environmental safety but not for its performance in agricultural systems, except if the action that the microbes exert in the rhizosphere is quick enough to induce the positive effect on plants, e.g., during the pathogen control of seedling diseases (Guyer et al. 2015; Quagliotto et al. 2009). Further studies are required to better characterize the ecological behavior of bacteria before their release to the soil.

6 Final Remarks

Plant-associated Pseudomonas are multifaceted bacteria, with a high metabolic diversity and interesting plant growth traits (Fig. 15.2). Even if there is no doubt regarding the benefits of Pseudomonas spp. inoculation on plant growth promotion, there is also a public concern due to their potential as opportunistic pathogenic agents. Thus, further knowledge and experience about their use in agroecosystems, in single or mixed formulation, will give insight to the potential use of Pseudomonas spp. in agricultural systems.

Fig. 15.2
figure 2

Fluorescent Pseudomonas: plant health and plant growth-promoting activities. Limitations in field performance and in registration process have delayed the wider commercial adoption of Pseudomonas-based inoculants. The improvement of commercial formulations and/or the coinoculation with other PGPR may overcome those drawbacks. Genetic modification (GM) is a more questionable alternative

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The adoption of sustainable agronomical practices for preservation of the native, active and adapted Pseudomonas populations in every location would reduce the need for reintroducing them as inoculants (Agaras et al. 2012).