Open access peer-reviewed chapter - ONLINE FIRST

Synthetic Communities of Bacterial Endophytes to Improve the Quality and Yield of Legume Crops

Written By

Mariela I. Monteoliva, Lucio Valetti, Tania Taurian, Clara S. Crociara and María Carla Guzzo

Submitted: September 19th, 2021 Reviewed: January 7th, 2022 Published: March 31st, 2022

DOI: 10.5772/intechopen.102519

IntechOpen
Legumes - Volume 1 Edited by Jose Carlos Jimenez-Lopez

From the Edited Volume

Legumes - Volume 1 [Working Title]

Dr. Jose Carlos Jimenez-Lopez and Dr. Alfonso Clemente

Chapter metrics overview

39 Chapter Downloads

View Full Metrics

Abstract

Plant-associated microbiomes confer fitness advantages to the plant host by growth promotion through different mechanisms including nutrient uptake, phytohormones production, resistance to pathogens, and stress tolerance. These effects of the potentially beneficial microbes have been used in a diversity of biotechnological approaches to improve crop performance applying individual bacterial cultures. However, healthy plants host a diversity of microorganisms (microbiota). Next-generation sequencing technologies have offered insights into the relative abundances of different phylogenetic groups in a community and the metabolic and physiological potential of its members. In the last decade, researchers have started to explore the possibilities to use temporal and functional combinations of those bacteria in the form of synthetic communities. In this chapter, we review the benefits of using endophytic bacteria in legumes, the available methodological approaches to study the effects of bacterial communities, and the most recent findings using synthetic communities to improve the performance of legume crops.

Keywords

  • sustainable agriculture
  • abiotic and biotic stresses protection
  • food security
  • endophytic bacteria
  • synthetic communities

1. Introduction

Plants constitute vast and diverse niches for endophytic organisms, and there is not a single plant species devoid of them. The most up-to-date definition for endophytes defines them as the microorganisms isolated from surface-sterilized plant tissues, which do not cause any noticeable harm to their host plants [1, 2]. The most abundant and common microbes living as endophytes are bacteria and fungi [3]. Endophytic bacteria are present in any kind of plant, from ferns and bryophytes to mono and dicotyledonous species [4]. In nature, mainly the intercellular spaces of the plant host are colonized by the endophytic bacteria [1, 5, 6]. But, endophytes have been also found in intracellular spaces of grapevine, barley, tobacco, Arabidopsis, and pine [7], suggesting that legumes may also have intracellular endophytes.

The endophytic bacterial communities make significant contributions to growth promotion and plant health in mutualistic (even symbiotic) relationships. The plant host protects the bacteria from the environment, while the endophytic community provides several benefits to the host. The benefits for the plant may include nutrient assimilation (such as nitrogen, phosphorus, or iron), growth stimulation, defense against pathogens, and/or protection against environmental stresses [8, 9]. Some of these effects might be altered when the plant is under stress [10].

The use of these natural symbionts/mutualists offers an opportunity to maximize legume crop productivity while reducing the environmental impacts of agriculture. For decades, most of the studies (and agricultural applications) have been about the effects of individual strains of bacteria, but recently with the bloom in bioinformatics and sequencing technology development, the knowledge about the plant microbiota has burst, and the potential to use and manipulate complex bacterial communities has started to be the target of a large research community.

Advertisement

2. Plant endophytic microbiome

In natural environments, the intracellular spaces of legumes are inhabited by numerous microorganisms, such as virus, fungi, nematodes, and bacteria. Here we focus on bacterial endophytes that benefit the plant in some way. Those bacteria colonize the host by several mechanisms, such as natural opening or injures and proliferate within the host. There is a huge taxonomic and functional diversity of endophytic bacteria, adapted to the microenvironments that the plant host provides. That diversity will be shaped by the microbial community members, the plant host, and the environmental conditions.

2.1 Colonization and distribution within the host plant

Colonization mechanisms vary with the type of interaction between the host and the bacteria and the life cycle of the microbe. Overall, most of the endophytic bacteria enter the plant through the roots. Since the microbial diversity decreases from the root to the leaves, it has been proposed that most of the microbes colonize the plant through the roots and proliferate to aboveground tissues [11] (Figure 1). Endophytic bacteria are usually “recruited” by plant host root exudates, such as organic acids, amino acids, and proteins [12, 13]. Once the bacteria are close to the root surface, they enter through lateral root emergence areas or other openings, caused by wounds or mechanical injuries. In the early stages, most of the endophytes are first observed in root hairs and subsequently in the root cortex [14]. However, endophytes can also colonize the leaves through the stomata, injuries in the epidermis, or introduced by vectors. In leaves, bacterial endophytes have been observed in the intercellular spaces of mesophyll, substomatal areas, and xylem tissues [15, 16].

Figure 1.

Diversity gradient of bacterial endophytic microbiota and growth promotion mechanisms to legumes. Legumes are surrounded and interact with bacteria in the soil and air (epiphytic bacteria in the rhizosphere and phyllosphere) and in the inter- and intra-cellular spaces (endosphere). Those bacteria can be saprophytic, pathogenic, or beneficial for the plant. The beneficial bacteria can promote plant growth by direct and indirect mechanisms. Direct mechanisms include phytohormone, volatiles, and other compounds production and facilitation of nutrient assimilation. Indirect mechanisms include pathogen and abiotic stress protection. ISR, induced systemic resistance.

In addition, the habit of the microbe conditions its colonization strategy. For example, obligate endophytes, which depend on the plant metabolic activity for their survival, are usually transmitted to the seed (vertical transmission) and spread inside the plant or through the action of a vector. On the contrary, most of the facultative endophytes, which have a free life in the soil and colonize the plant during some stage of their life cycle, colonize the plant through occasional wounds [17].

The colonization process itself alters host plant physiology (in a process called “niche construction” from the microbe’s point of view) by defense alterations or direct shift of the host metabolism [18]. Those microenvironment changes can affect the local microbiome structure and functions, by altering relationships among bacterial species and within the host. Furthermore, under particular conditions, part of the response of the plant will stimulate or recruit specific endophytes, which may contribute to survival or tolerance of that condition [19, 20]. It was proved in tomato cultivars that the transplant of the rhizosphere from a resistant to a susceptible cultivar suppressed Ralstonia solanacearumdisease symptoms. They found a highly abundant flavobacterial genome in the resistant cultivar rhizosphere, and the isolated flavobacteria suppressed disease symptoms in the susceptible cultivar in pots [21]. In legumes, it was reported that Fusarium-resistant common bean cultivars showed a higher abundance of Pseudomonadaceae, Bacillaceae, Solibacteraceae, and Cytophagaceae families [22], but no further inquiries have been reported.

Another aspect affecting the colonization process of the endophytic bacteria is the host defenses. Endophytes live in the same environment as many plant pathogens and share close similarities with them. Microbe- or pathogen-associated molecular patterns (MAMPs/PAMPs) are conserved and necessary for microbial survival, but plants have evolved multiple receptors to recognize them and induce the plant immune system. Then, the colonization of endophytic bacteria triggers plant defenses, and the process needs to be avoided or blocked by the beneficial endophytes to be able to colonize and proliferate within the host [2, 23, 24]. It is not well understood yet how the beneficial bacteria overcome the defenses, but a few mechanisms have been unraveled, including the blockage of MAMPs and defense signaling [25]. The beneficial bacteria Bacillus subtilisavoid a strong defensive response in the host by blocking the detection of their own flagellin by the secretion of the flagellin-binding peptide subtilomycin [25, 26]. Another mechanism is the secretion of bacterial antioxidant enzymes, such as superoxide dismutases and glutathione-S-transferases to detoxify the reactive oxygen species that signals the plant defense [27]. An alternative mechanism is the suppression of salicylic acid (SA)-mediated defense signaling. Sinorhizobium frediiHH103 with defective type III secretion system (T3SS) is unable to suppress SA-dependent defenses and subsequently fails to promote nodulation on the host [28], indicating that the suppression of the SA-dependent defense is critical for endophyte colonization. Some of those mechanisms have not been reported in legumes, but if those bacteria are colonizing legumes, similar mechanisms might be in action.

The establishment of the endophytic bacterial community in the legume host is a complex and dynamic process that has been studied mostly in fragments and simplified systems (usually one bacterial strain in one host under one or a few conditions), and it must be further understood to take the best advantages of their potential benefits for legume agriculture.

2.2 Endophytic bacterial diversity

There is an enormous diversity of bacterial endophytes in legumes, considering that the rhizobia are also endophytes. The interaction of rhizobia and legumes has been studied for more than a century [29]. Since then, many rhizobial endophytic bacteria were isolated from different legumes, particularly root and nodule tissue. These bacteria can establish a symbiotic interaction, induce the formation of new organs in roots and stems called nodules, and fix atmospheric nitrogen. In addition, the so-called “new rhizobia” (or noncanonical rhizobial genera) of Alfa- and Beta-Proteobacteria has been reported in the last decades. They can form nodules and fix nitrogen and mainly belong to Microvirgaspp. and Burkholderiaspp., respectively [30]. Other non-nitrogen-fixer endophytes are present in nodules and sometimes improve nodule formation [31, 32, 33]. For instance, Hoque et al. [34] isolated rhizobia and non-rhizobia endophytes from two wild Acaciaspecies from Australia, and nodules were produced by species of the genera Rhizobium, Ensifer, Mesorhizobium, Burkholderia, Phyllobacterium, and Devosia, much more than expected. In addition, rhizobial species were isolated from other plant tissues apart from nodules [3].

Overall, from a large number of bacterial genera present in legumes, the most frequent ones (excluding rhizobia) are Agrobacterium, Bacillus, Enterobacter, and Pseudomonas, followed by Acinetobacter, Arthrobacter, Curtobacterium, Devosia, Dyella, Herbaspirillum, Klebsiella Micromonospora, Microbacterium, Mycobacterium, Ochrobactrum, Paenibacillus, Pantoea, Rhodopseudomonas, Serratia, Staphylococcus, and Sphingomonas([3, 9, 21], and reference therein) (Tables 1 and 2).

Legume speciesOrganTreat.MethodMost abundant bacterialFunctionsRef.
Peanut
Arachis hypogaea
Seed germs, sprout, cot.Develop.16SSynechococcus; Halothiobacillus, Paracoccus, Agrobacterium, Gallionella; Mycobacterium, Rhodococcus, Burkholderia, Erwinia, Hyphomonas, DevosiaN.D.[35, 36]
RootMonocrop vs. crop rotationMG, MTBordetella, Burkholderia, Ktedonobacter, Ktedonobacter racemifer, Opitutus terrae, Thermomicrobium roseum, Chloroflexus aggregans, Thermosediminibacter oceani, Dehalogenimonas lykanthroporepellensN, S, P metabolisms, oxidative stress resistance, antibiotics, siderophores, IAA synthesis genes[37]
Chickpea
Cicer arietinum
Roots, noduleBT-transgene16SCalothrix, Rickettsia, Mesorhizobium, Methylobacillus, Arthrobacter, Bacillus, Streptomyces, Saccharopolyspora, Rhodococcus, Ramlibacter, Propionivibrio, Janthinobacterium, Kaistobacter, Sphingomonas, Ammoniphilus, Rubrobacter. Actinocatenispora, Pseudaminobacter, Burkholderia Shinella.N.D.[38]
Rosewood
Dalbergia odorífera
NoduleSeedlings, rhizobial inoculation16SBradyrhizobium, Chloroplast norank, Lactococcus, Mycobacterium, Bacillus, Rhizobium, Mesorhizobium, BurkholderiaN.D.[39]
Soybean
Glycine max
NoduleSalty soils16SEnsifer, Enterobacter, Stenotrophomonas, ChryseobacteriumN.D.[40]
RootSoil type16SKlebsiella, Pseudomonas, Stenotrophomonas, Rhizobium, Acinetobacter, Chryseobacterium, Acidovorax, Achromobacter, Agrobacterium, BurkholderiaIAA, BNF, P solubilization, ACC-DA[41]
Strigolactone-related genes16SMicrobacteriaceae, Rhizobiaceae, BdellovibrionaceaeN.S.[42]
Root, nodule, soilDevelop., soil type16SProteobacteria, Actinobacteria, Firmicutes and BacteroidetesN.D.[43]
Develop.16SBacillus, Bradyrhizobium, RhizobiumN.D.[6]
Alfalfa
Medicago sativa
NoduleSynthetic community16SBrevibacillus, Paenibacillus, Pantoea, PseudomonasAntibiotics[44]
16S, nodC, nodA, nifH genesSinorhizobium, Rhizobium, Bacillus Shinella, Pseudomonas, Variovorax, Novosphingobium, Methylibium, Bradyrhizobium, MycobacteriumN.D.[45]
Medicago truncatulaLeaf, nodule, rootGenotype, soil16S,MGPseudomonas, Niastella, cyanobacteria Phormidium. Thioalkalibacter, Neorhizobium, Ohtaekwangia, Nodules: Ensifer, Rhizobium, Bradyrhizobium, Rhizobacter, ShewanellaN.D.[46]
Pea
Pisum sativum
Root, noduleDevelop.16SRizhobium Mezorizhobium, PseudomonasBNF[47]
Black mung bean
Vigna mungo
NoduleFull-length 16SFerrmicutes. B. subtilis, Paenibacillus taichungensisP solubilization, IAA, siderophore, ammonia, HCN, ACC-DA[48]
18S, 16SCandida glabrata, C. tropicalisIAA, ACC-DA, siderophores, ammonia, polyamines synthesis[49]
Mung bean
V. radiata
Nodule16SBacillus aryabhattai, Bacillus megaterium and B. cereusIAA[50]
Cowpea
Vigna unguiculata
Nodule16SRhizobium, Paraburkholderia, Enterobacter, Strenotrophomonas PseudomonasBNF[51]
Red clover
Trifolium pratense
Root16SRhizobia, Pantoea, Sphingomonas, Novosphingobium, PelomonasN.D.[52]
Lens culinaris, P. sativum (plus canola and wheat)RootSpecies, soil type16SPseudomonas, Arthrobacter,unclassified genera of Enterobacteriaceae, ComamonadaceaeN.D.[53]
A. hypogaea, G. max, V. radiata, V. unguiculata, V. mungoNodule16SEnterobacter cloacae, E. ludwigii, Chryseobacterium indologenes, Klebsiella pneumoniae, Klebsiella variicola, Pseudomonas aeruginosa.BNF, P solubilization, siderophores, IAA, ACC deaminase (nifHgene)[54]
Vicia villosa, T. repens, T. pretense, M. sativaSeed16S,MGAcinetobacter, Sphingomonas, Lactobacillus, Bacillus, Pantoea, SalmonellaEnergy, amino acid and carbohydrate metabolisms, cell growth and death programs, transport, genes[55]

Table 1.

Culture-independent studies of the endophytic bacterial microbiome in legume crops.

ACC, 1-aminocyclopropane-1-carboxylate; ACC-DA, ACC deaminase activity; IAA, indole-acetic acid; BNF, biological nitrogen fixation; Develop., developmental stages; MG, meta-genomics; MT, meta-transcriptomics; N.D. not determined; N.S., not significant; Treat, treatment or factor affecting microbiome.

Legume speciesOrganTreat.Met.Most abundant bacterialFunctionRef.
Peanut
Arachis hypogaea
NoduleGenotype16SRhizobium phaseoli, Bacillus tequilensis, B. altitidinus, B. tequilensis, B. siamensis, B. subtilis, Pantoea dispersa, Paenibacillus illinoisensis, Kosakonia oryzendophytica, Rhizobium mayense, P. dispersaIAA; ACC-DA; P, Zn, and Si solubilization, siderophore[56]
Seed16SPseudomonasspp.IAA, P solubilization, siderophores, cellulase, protease, control of S. rolfsii[57]
Chickpea
Cicer arietinum
RootSoil type16SEnterobacteriaceae, Pseudomonadaceae, Xanthomonadaceae, Bacillus, Stenotrophomonas, Pseudomonas, EnterobacterN.D.[58]
Root, nodule16SMcrobiospora, Streptomyces, Micromonospora, ActinomaduraN.D.[59]
16SEnterobacter, Rhizobium, Stenotrophomonas, Pseudomonas, Burkholderia, Bacillus, BrevibacillusIAA, siderophores[60]
Soybean
Glycine max
NoduleAntifungal activity16SEnterobacter, Acinetobacter, Pseudomonas, Ochrobactrum, BacillusBNF, IAA, siderophore[61]
Leaf, stem, rootRR-transgene16SEnterobacter ludwigii and Variovorax paradoxusIAA, P solubilization[62]
Leaf, stem, root, nodule16S
nifH
Pseudomonas aeruginosa and BradirizhobiumIAA, P and Zn solubilization, siderophore, ACC-DA, cell wall degrading enzymes, pathogenicity[63]
Lentil
Lens culinaris
Nodule16SPseudomonas stutzer, Lysinibacillus pakistanensis,N.D.[64]
Common bean
Phaseolus vulgaris
Roots16SBacillus velezensis Bacillus amyloliquefaciens Bacillus halotolerans,Bacillus mojavensis,Bacillus methylotrophicus, Bacillus subtilus Pseudomonas frederiksbergensis Pseudomonas lini, Agrobacterium fabrum Glutamicibacter halophytocola.IAA, P solubilization, siderophores, HCN, xylanase chitinase, lipopeptide genes, antifungal activity[65]
Cowpea
Vinga unguiculata
Nodule16SRhizobium, Paraburkholderia Enterobacter, Strenotrophomonasand PseudomonasBNF[51]
C. arietinum, Pisum sativumNodule,
root
16S,RFLPPantoea agglomerans, Bacillus cereus,B. sonorensis, B. subtilis, Pseudomonas chlororaphis, Ornithinibacillussp., Ochromobacteriumsp.,IAA, P solubilization, siderophores, ammonia, organic acids, HCN, biocontrol[66]
Crotalariaspp.,
Indigoferaspp.
Erythrina brucei
NoduleGenotype16SAchromobacter, Agrobacterium, Burkholderia, Cronobacter, Enterobacter, Mesorhizobium, Novosphingobium, Pantoea, Pseudomonas, Rahnella, Rhizobium, Serratia, and Variovorax. Bacillus, Paenibacillus, Planomicrobium,and Rhodococcus.N.D.[67]
V. mungo,
V. radiata
Stem16SEnterobacter, Bacillus, Pantoea, Pseudomonas, Acromobacter, OcrobacteriumBNF, IAA, P solubilization, siderophores, antifungal activity[68]
P. sativum,
V. faba
Nodule16S, nodCRhizobium leguminosarum, R. indigoferae, R. hidalgonense, R. sophorae, R. laguerrea, R. acidisoli, R. anhuiense,IAA, P solubilization, siderophores[69]
A. hypogaea,
G. max,
V. radiata,
V. unguiculata,
V. mungo
Root nodule-16S nifHEnterobacter cloacae, Chryseobacterium indologenes, Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter ludwigiiy, Klebsiella variicolaBNF, P solubilization, AIA, siderophores, ACC-DA[54]
Trifolium, Lupinus, Ornithopus, Scorpiurus, Medicago, Trifolium, ViciaRootField sites16SMicrobacterium, Chryseobacterium, Bacillus, Paenibacilus, Staphylococcus,Pantoea, Erwinia, Achromobacter, Lelliotia, Enterobacter, Acinetobacter, Janthinobacterium, Pseudomonas, Stenothrophomonas, Serratia, RahnellaIAA, P solubilization, siderophore, cellulase[70]
Anthyllis, Colutea, Cytisus, Lathyrus, Lotus, Lupinus, Medicago, Melilotus, Ononis, Ornithopus, Robinia, Trifolium, Vicia, WisteriaNoduleEcoregions (Belgium)16SBacillus, Paenibacillus, Arthrobacter, Microbacterium, Rhodococcus, Sphingomonas, Cohnella, Pseudomonas, Herbaspirillum, Pantoea, Corynebacterium, Chryseobacterium, Sphingomonas and XanthomonasN.D.[31]

Table 2.

Culture-dependent studies of the endophytic bacterial microbiota in legume crops.

ACC, 1-aminocyclopropane-1-carboxylate; ACC-DA, ACC deaminase activity; IAA, indole-acetic acid; BNF, biological nitrogen fixation; Develop., developmental stages; MG, meta-genomics; MT, meta-transcriptomics; N.D. not determined; N.S., not significant; Morph & Bioch., morphological and biochemical characterization, Treat, treatment or factor affecting microbiome.

2.3 Factors affecting diversity

The composition, diversity, and abundance of the endophytic microbiome are influenced by the soil microbial pool; the plant host identity and status (genotype, development, and physiology); agricultural practices; and climate and environmental conditions (such as temperature, water supply, and nutrients) [8, 16, 71]. Comparisons among plant species (canola, wheat, pea, and lentil) in different locations and soil types pointed to the genotype influence as the highest effect determining endophyte diversity ([72] in Table 1). However, when considering close Medicagogenotypes (intraspecies comparison), the host genotype effect was not significant (1% of contribution to the total variance), but both soil and plant genotypes were significant for the root microbiota diversity [53]. In the case of the leaf microbiome, the soil reduces its relative importance, since some bacteria colonize it from underground organs, but others enter through stomata or vectors [46]. Broadly, the soil limits the available microbial pool, while the host genotype is a relevant barrier for colonization. Agricultural practices could directly affect the microbiome by chemical applications or through changes in the host physiology. The effects of biotic and abiotic factors shaping the endophytic bacteria communities in plants were reviewed by Papik et al. [73]. In addition, the actual diversity could be masked by the method used to describe it (such as culture-dependent or -independent, see Section 2.4) [16].

2.4 How to study microbiome diversity

Natural communities of endophytic bacteria are conventionally studied using culture-dependent and -independent methods [74]. Culture-dependent methods imply the extraction of the microbes and their growth in synthetic media. Those strategies allow to isolate the microbe and further study them in vitroand in manipulative experiments, but they strongly underestimate the number of bacteria (and the diversity of the community), as cultivable bacteria usually represent only 0.001–1% of the actual bacteria in a sample [16, 75]. Recently, Hartman et al. [52] isolated 200 bacteria strains that represent ~20% of the most abundant genera in Trifoliumroots, which was one-quarter of the ~3500 detected OTUs in a manageable effort to increase the cultivated endophytic bacteria from a legume (Table 1).

On the other side, culture-independent methods mostly rely on the extraction of bacterial genetic material from plant tissues. The genomic DNA can then be analyzed using a range of molecular fingerprinting techniques such as Amplified rDNA Restriction Analysis, Gradient Gel Electrophoresis, and Terminal Restriction Fragment Length Polymorphism (RFLP) [16]. In recent years, DNA fingerprinting techniques have been set aside by more advanced molecular techniques. Those new methods involve DNA extraction from the entire bacterial population to sequence a specific phylogenetic marker, such as the 16S rRNA gene, or the whole genome [76]. In addition, using RNA instead of DNA, it is possible to detect active functional diversity, which provides information about the transcriptionally active functions, as well as the massive analysis of proteins (peptides) or metabolites (by high throughput analysis of “omics”). The latter two do not provide taxonomic information but a functional one.

The sequence-based methods allow a deeper analysis of the endophytic diversity than traditional fingerprinting, although some of the species with low abundance might be still missed. To minimize those losses, it is important to sequence with high depth and carry out rarefaction analysis (to check that the OTU versus the diversity or richness reaches the plateau). Other technical considerations for sequencing analysis are discussed in detail by Lucaciu et al. [77].

The bacterial diversity of the microbiome can be described taxonomically and functionally by different approaches. The most traditional strategy is the taxonomic description of the diversity, which identifies the species present in the microbiome and quantifies their abundance by genome or specific gene sequencing. From that data, researchers have started to uncover what is known as the “core microbiome” [78], which is defined as the group of species present in one plant across different genotypes, environments, developmental stages, etc. Depending on the scale of the analysis, a higher or lower number of species are shared among them. For instance, if dicot and monocot species are compared, the number of shared species will be lower than if two cultivars of the same species are compared in the same environment. A core endophytic microbiome of roots of red clover (Trifolium pratense) includes 70% of Rhizobia, and it was dominated by the genera Pantoea, Sphingomonas, Novosphingobium, and Pelomonas[52] (Table 1). Glycinespp. nodules showed a majority of Ensifergenera, followed by Enterobacter, Stenotrophomonas, and Chryseobacterium(>0.5%), and some nonrhizobial bacteria only in soybean (Glycine max), including Enterobacter cloacae(3.62%), Stenotrophomonassp. CanR-75 (2.79%), and Stenotrophomonas maltophilia(2.41%) [40] (Table 1). Overall, little is known about the core endophytic microbiome in legumes, although some core rhizospheric microbiomes have been described (e.g., [79]).

In addition to the core microbiome, the “keystone” species have been described [80]. Keystones are highly connected species that largely change the structure and function of the microbiome when removed. They may be predicted by co-occurrence networks (by correlation analysis) and are defined as those whose abundance highly correlates with most of the other species [81]. Those correlations can be positive or negative (i.e., two species are always together or the presence of one excludes the other), and the interaction between each other may be indirect (for instance, mediated by a change in the host) [82]. It has been predicted that when the keystone species is missing, the abundance and proportion of the community change, and occasionally, one species may extremely proliferate over the others. Knowing which are the keystone species for one host is critical to effectively design any agricultural management strategy to protect a healthy microbial community and improve the fitness of the crop.

A second strategy to characterize the microbiome is the functional description, based on the metabolic functions present in the microorganisms. According to the previous model (with a core microbiome and keystone species), the communities in the microbiome are built to occupy functional niches [81]. This means that one species might be (at least partially) replaced by another one, which provides the same function to the community and/or the host. Those key functions of a particular species are given by a set of genes that allow the microbe to effectively interact and benefit the rest of the microbial community and the plant host under specific conditions. These functional traits can be screened and studied by any “omic” analysis and then grouped by the presence of specific metabolic functions (see [83, 85] in Table 1). For instance, the most important genes differentially detected in the rhizosphere of pea (Pisum sativum) under different tillage and fertilization treatments were genes coding ABC transporters and secretion systems, transcription factors, peptidases, methane metabolism, quorum sensing, and bacterial motility proteins [85]. To understand which services the microbial community provides and may favor the host plant, the functional analysis may be more useful than a taxonomic-only approach. However, both are necessary and provide valuable information about the microbiomes.

Advertisement

3. Benefits of endophytic microbiota to the host plant

Once within the plant, endophytes might provide several benefits. We grouped them into three different kinds: direct growth promotion, protection against pathogens, and protection against abiotic stress (Figure 1).

Direct promotion occurs when endophytes stimulate shoot and/or root growth by increasing the availability of limiting nutrients or producing compounds that directly stimulate growth. On the other hand, indirect promotion occurs when the endophytes can protect the plant against diseases, pests, or environmental stress, indirectly improving the host performance [86]. The molecular mechanisms and pathways are not exclusive for each direct or indirect growth promotion effect. A single endophytic bacterial strain may have more than one of these plant-growth-promoting traits (e.g. [37, 41, 48, [49, 55] in Table 1, and [56, 57, 63, 65, 66, 68] in Table 2).

3.1 Increase of nutrient availability

The main mineral nutrients required for plant growth are nitrogen, phosphorus, and iron. There are numerous plant-growth-promoting microorganisms able to increase their availability, and some mechanisms have been determined.

3.1.1 Biological nitrogen fixation (BNF)

Nitrogen is crucial for plant growth and health. Approximately 30–50% of the N in crop fields results from BNF by soil microorganisms. The ability to fix atmospheric nitrogen (N2) is present in various bacterial species that are either free-living or endophytically associated with plant roots. BNF is the most and long-term studied plant-growth-promoting effect of soil microorganisms in legumes [87, 88]. Other plant growth promoter bacteria genera, different from rhizobia, are also able to enhance the acquisition of N by legumes. Anzuay et al. [89] and Taurian et al. [90] observed that endophytic bacteria belonging to Serratia, Acinetobacter, Bacillus, and Enterococcusenhanced peanut (Arachis hypogaea) N content. Dey et al. [91] reported that the increase in the number of nodules in plants inoculated with growth promoter bacteria could be attributed to the enhancement of root growth and root length. This enhancement provides more sites for nodulation by rhizobial strains in the soil. Furthermore, since BFN is a highly demanding ATP process, phosphorus is a critical nutrient for legumes.

3.1.2 Phosphate solubilization and mineralization

Even in phosphorus-rich soils (such as phosphate-fertilized soils), most of this element is in insoluble forms, and only a small proportion (~0.1%) is available to plants [92]. The solubilization of phosphates in the rhizosphere is one of the most common modes of action of growth promoter microbes that enhance nutrient availability to plants [93]. Phosphate-mineralizing and phosphate-solubilizing bacteria (PMB/PSB) secrete phosphatases and organic acids to convert insoluble phosphates (organic and inorganic) into soluble monobasic and dibasic ions [93]. Among legume endophytes, there are several phosphate-solubilizing bacteria able to promote plant growth, and some studies demonstrated that plant growth promotion was directly correlated with the increase of P in the plant tissues [89]. Soybean and peanut endophytes solubilize mineral phosphate [90]. In addition, several studies described endophytic bacteria with phosphate-solubilizing/-mineralizing ability that increase legume growth [89, 90, 94, 95]. The inoculation of pea with phosphate-solubilizing Pseudomonasspp. isolated from this legume, enhanced the plant biomass [96]. Pantoeaspp. isolated from root nodules of peanut showed a strong phosphate-solubilizing activity [97]. However, the inoculation of phosphate-solubilizing bacteria isolated from peanuts did not promote growth when they were inoculated in the rapeseed culture [98]. These results point to a specific plant-bacteria interaction that directly affects the ability to promote growth or the efficiency of the mechanism.

The main phosphate-solubilizing mechanism in Gram-negative bacteria involves the bacterial PQQ cofactor, described as essential in P nutrition and plant growth. Mutation in the pqqHgene from Pseudomonas fluorescenscaused the loss of the phosphate-solubilizing phenotype and plant growth promotion ability on tomato plants [99]. In legumes, Ahmed and Shahab [100] observed that a non-producing-PQQ bacteria (which lost the phosphate solubilization ability) showed a decrease in the growth promotion of bean plants. On the contrary, Ludueña et al. [101] determined that in the non-producing PQQ strain Serratiasp. promoted the growth of peanut at a similar level to the wild type, indicating that PQQ is not essential for growth promotion.

3.1.3 Iron uptake

Iron is essential for all living organisms, and its bioavailability in the soil is limited. Siderophores are small molecular compounds, secreted by microbes, which chelate iron in the soil and generate soluble complexes that can be absorbed by plants [97]. Microbial siderophores’ secretion directly stimulates plant growth by increasing the availability of iron in the soil surrounding the roots [102]. Plants lacking soil bacteria suffered from iron deficiency [103]. Therefore, this mechanism helps plants to thrive in low-iron soils. The inoculation of black mung bean (Vigna radiata) with the siderophore-producing endophyte, Pseudomonassp. GRP3, reduced iron deficiency and chlorotic symptoms and increased the content of chlorophyll a and b [104]. Furthermore, since diazotrophic organisms require Fe+2 and Mo+2 factors for the functioning and synthesis of nitrogenase, iron solubilization by microbes also improved nitrogen fixation in legumes [105]. Native peanut isolates produce siderophores together with other plant-growth-promoting traits, increasing peanut growth and performance [106].

3.2 Phytostimulators

Endophytic bacteria directly promote plant growth by the production of phytohormones, such as auxin or cytokinin, or by lowering the plant ethylene (ET) levels. By these mechanisms, bacterial endophytes can also accelerate seedling emergence and promote plant establishment under adverse conditions.

3.2.1 Phytohormone-like molecule production

The production of phytohormones-like compounds is considered an important trait of endophytes that positively affects the growth and development of many plants including legumes [8, 10, 107]. Thus, changes in plant growth frequently reflect alterations in phytohormone levels induced by endophytes [3]. But, even when production of these compounds by growth promoter microbes has been demonstrated, that effect cannot be unequivocally attributed to them.

The five main phytohormones produced by bacteria are auxins, cytokinin, gibberellins, ET, and abscisic acid (ABA). It has been postulated that genes encoding biosynthesis of the auxins, cytokinin, and gibberellins are often present in the metagenome of plant endophytic bacterial communities [108]; however, it has not been yet explored in legumes using any omics approach (ET and ABA are discussed in Section 3.4.3).

Among these growth regulators, auxins are the most studied. These compounds affect plant growth by inducing cell enlargement and division, root development, apical dominance, increase growth rate, photo- and geo-tropism [109]. The production of auxin-like compounds increases seed production and germination along with increased shoot growth and tillering. Within these compounds, indole-acetic acid (IAA) is the most frequent and indeed most studied phytohormone in growth promoter bacteria. IAA produced by endophytic bacteria is one of the most relevant and studied effector molecules in growth promotion, pathogen defense, and plant-microbe interactions [104]. For instance, rhizobia from soybean, pea, and faba bean nodules not only fix nitrogen and produce siderophores, but also auxins (see Refs. [54, 110] in Tables 1 and 2, and [61]). IAA can be synthesized directly by plant-associated microbes, and ~ 80% of the rhizosphere bacteria may produce IAA [69, 111]. For instance, it could be produced by Alcaligenes, Azospirillum, Pseudomonas, Pantoea, Rhizobium, and Enterobacterin the presence of L-tryptophan as a precursor, although there are other pathways and a variety of auxins, such as indole-3-butyric acid (IBA), indole-3-pyruvic acid (IPA), or tryptophol (TOL), which are also produced by growth promoter bacteria [112].

Cytokinins are another group of growth-stimulating phytohormones that are responsible for cell division, plant senescence, seed germination, flower and fruit development, and apical dormancy [113, 114]. Although cytokinins are produced by several growth promoter microbes, few studies have demonstrated their beneficial effects.

Gibberellins are involved in many developmental processes in plants, such as flowering regulation, seed germination, stem and leaf elongation [114], but also the promotion of nodule organogenesis and the negative regulation of the rhizobial infection and root system development [115].

Several bacteria produce and regulate the production of more than one phytohormone, such as the rhizobacteria Bacillus aryabhattai, which produces ABA, IAA, cytokinin, and gibberellic acids in vitroand promotes soybean growth [116]. Thus, inoculation with endophytic bacteria may benefit legumes via the production or suppression of some phytohormones.

3.2.2 Volatile compounds and other phytostimulators

Some growth promoters’ bacteria can regulate plant growth by releasing volatile compounds [86]. For instance, B. subtilis, Bacillus amyloliquefaciens, and E. cloacaepromote plant growth in legumes by releasing volatiles, such as 2,3-butanediol and acetoin [117, 118], while the mutants of B. amyloliquefaciensIN937a and B. subtilisGB03, blocked in their biosynthesis, did not promote Arabidopsis growth [118]. Studies on growth promotion by Chryseobacteriumrhizoplane in mung bean indicate that 2,3-butanediol is the molecule causing growth stimulation [119]. Growth promotion mechanisms of volatiles in plants were reviewed by Sharifi and Ryu [120].

Other nonvolatile molecules such as bacterial cell components or secreted compounds have been proposed to be plant growth stimulators. The endophyte Serratia proteamaculanswas able to promote soybean growth by the production of a lipo-chitooligosaccharide [121]. And the PQQ peptide, previously mentioned to be associated with P solubilization, has also shown growth promotion [99], antifungal activity, and the ability to induce systemic resistance [86]. The role of PQQ in plant-microbe interaction has been reviewed by Carreño-Lopez et al. [122].

Lastly, endophytes can generate allelopathic effects inhibiting the growth of neighboring plants or protecting the host plant from allelopathic effects from adjacent plants [123]. For example, endophytic bacteria of red clover seem to be responsible for the negative allelopathic effects observed over maize, reducing seedling emergence and height [124]. Additionally, some weeds have negative allelopathic effects on legumes, mediated by their endophytic bacteria, which inhibit nodulation [125].

Overall, there is a body of evidence that suggests that enhancing or regulating phytohormone or other phytostimulators via endophytic microorganisms is a viable strategy to increased crop production in agriculture [108], and because of these attributes, endophytes have gained ground in the area of agricultural sustainability.

3.3 Protection against pathogens

Among the major factors restraining agriculture are crop diseases and pests, while one important driver of plant health is the structure and dynamics of the plant-associated microbial communities [126]. In recent years, a deeper understanding of the endophytic microbiome and its potential has been achieved to become a fundamental tool in phytosanitary management and reduce the damage of plant diseases.

Endophytes can decrease the harmful effects of pathogens by different mechanisms, including direct and indirect mechanisms [104]. Direct inhibition of pathogens is mainly mediated by the synthesis of inhibitory allelochemicals such as antibiotics, hydrogen cyanide, iron-chelating siderophores [127], secretion of lytic enzymes, or quorum quenching (QQ) by degrading pathogens autoinducer signals [128]. Indirect biocontrol mainly includes the induction of the plant systemic resistance that inhibits the proliferation of a broad spectrum of phytopathogens [129].

3.3.1 Antibiosis

Most endophytes have been reported to produce secondary metabolites, and some of them exhibit antibacterial and antifungal properties, which help to inhibit the growth of phytopathogenic microorganisms [44]. Many metabolites with antimicrobial properties synthesized by endophytes have been described so far, such as flavonoids, peptides, quinones, alkaloids, phenols, steroids, terpenoids, and polyketides. Antimicrobial properties of bacterial metabolites were recently reviewed [130]. Hansen et al. [131] studied the microbiome of alfalfa (Medicago sativa) nodules and identified two families of molecules produced by Brevibacillus brevis in planta, such as antibacterial thyrozidines, and a new set of gramicidin-like molecules, britacidins. They conclude that, in addition to nitrogen fixation, it is likely that legume root nodules are also a source of active antimicrobial production.

3.3.2 Lipopeptides

Lipopeptides are low-molecular-weight cyclic peptides attached to a hydrophobic fatty acid. These molecules are classified into three families: surfactin, iturin, and fengycin. Iturins and fengycins show strong antifungal activities while surfactins exhibit strong antibacterial activity. Antimicrobial lipopeptides can form toroidal-like pores on cell membranes leading to membrane permeation and/or disintegration and protect plants directly suppressing the growth of pathogens or inducing systemic resistance [132]. Recently, 263 different lipopeptides were synthesized by 11 microbial genera, with Bacillusbeing the most abundant [133].

The common bean root microbiome was used to search potential biocontrol agents of Fusariumsp., Macrophominasp., and Alternariasp. fungi, causal agents of root rot disease [65]. Biocontrol assays conducted under controlled conditions demonstrated that B. amyloliquefaciens, B. halotolerans, Bacillus velezensis, Agrobacterium fabrum,and Pseudomonas linidisplayed the highest protective effect, and lipopeptide biosynthetic genes encoding surfactin, iturin, bacillomycin, and fengycin were present. These bacteria can produce at least one or more lipopeptides that may be involved in biocontrol activity.

3.3.3 Lytic enzymes

During plant colonization, endophytes produce numerous enzymes, which successively aid the hydrolysis of the plant cell wall. There are numerous types of enzymes such as chitinases, cellulases, hemicellulases, and 1,3-glucanases [70, 134]. These enzymes are also capable of degrading fungal (and oomycetal) cell walls hyphae, spores, and sporangia, thus contributing to the protection of the plant. The isolate Pseudomonasspp. EGN 1 was the most promising bioagent for the management of the stem rot (Sclerotium rolfsii) in groundnut, mediated by an important protease and cellulase production [57]. While, Brigido et al. [135] evaluated the diversity and functionality of the endophytic bacterial strains in the roots of native legumes from two different sites in Portugal, finding 15 isolates with a high cellulase production.

3.3.4 Hydrogen cyanide

A few bacterial species are known to produce and excrete hydrogen cyanide, a potent inhibitor of cytochrome c oxidase and several other metalloenzymes [136]. The host plant is unaffected by the bacteria or the hydrogen cyanide produced by it. For this reason, hydrogen-cyanide-producing bacteria have an application as biological control agent. Zaghloul et al. [137] isolated a total of 167 endophytic bacterial from roots, nodules, leaves, and stems of faba bean (Vicia faba), pea, fenugreek (Trigonella foenumgracum), lupine (Lupinusspp.), common bean (Phaseolus vulgaris), and rice (Oryza sativa) at flowering stage. About 82% of the isolates showed positive results of hydrogen cyanide production. In another recent investigation, ~20 endophytic bacteria isolated from roots and nodules of chickpea (Cicer arietinum) and pea showed HCN production [66].

3.3.5 Siderophores

As previously mentioned, siderophores chelate iron in the soil making it more available for plants. Furthermore, by tightly binding the iron, siderophores reduce its bioavailability for plant pathogens and facilitate the death of the phytopathogens [138]. Some of the siderophores are known to be produced by endophytes, such as hydroxymate, phenolate, and/or catecholate types, confer biocontrol activities [139]. Also, the role of siderophores as part of the protective effect of the induced systemic resistance has been described in many studies. The production of siderophores is very common among Pseudomonas, Frankia, Streptomycessp. Several researchers described endophytic bacteria producing siderophores isolated from different legumes as peanut, faba bean, soybeans, chickpea, pea, and bean [65, 66]. Bahroun et al., [140] demonstrate that Rahnella aquatilisB16C, Pseudomonas yamanorumB12, and P. fluorescensB8P isolated from faba bean nodules suppressed Fusarium solaniroot rot in three faba bean cultivars in greenhouse. The three strains were able to produce siderophores and significantly reduced the disease severity. Zhao et al. [54] obtained 276 isolates from root nodules of soybean, six of which showed antagonistic to the pathogenic fungus Phytophthora sojae01. The isolates were identified as Enterobacter, Acinetobacter, Pseudomonas, Ochrobactrum, and Bacillusgenera. The high correlation of siderophores production and the fungal inhibition of nodule endophytic bacteria in that study supported the idea that the ferrous absorption by endophytic bacteria may be a viable inhibitory mechanism.

3.3.6 Quorum quenching

The regulation of gene expression in response to fluctuations in cell-population density is known as “quorum sensing.” Many important bacterial processes are regulated by it. Quorum sensing regulates gene expression depending on the accumulation of a signal molecule in the environment. The signal, called autoinducer, allows the bacteria to perceive the existing population density and jointly executed responses. Gram-negative bacteria use acyl-homoserine lactone (AHL) as an autoinducer, whereas Gram-positive bacteria utilize modified peptides [141]. The bacterial quorum sensing controls a wide variety of physiological processes such as virulence, extracellular polymeric substances (EPS) production, mobility, and biofilm formation among others, which are essential for the establishment of a pathogen in the host plant [142].

Often endophytic bacteria can disrupt quorum sensing. This ability to interfere with bacterial cell-to-cell communication was collectively called “quorum quenching” and can be crucial to prevent the plant colonization by pathogenic bacteria that use quorum sensing to coordinate virulence [143]. Several chemicals and enzymes have been identified that target the key components of bacterial quorum-sensing systems in the recent years (such as [33]). The mechanisms of quorum quenching may be the inhibition of the signal synthesis or detection, signal enzymatic degradation (by enzymes such as AHL acylase, AHL lactonase, and oxidoreductases), or synthesis of structural analogs of the signal [144]. Lopes et al. [145] reported antimicrobial activity against Pseudomonas syringaepv. tabaci or Hafnia alvei071 in endophytic bacteria isolated from common bean. The isolates Microbacterium testaceumBAC1065, BAC1100, and BAC2153, Bacillus thuringiensisBAC3151, and Rhodococcus erythropolisBAC2162 exhibited a greater ability to inhibit the response of AHL reporter.

3.3.7 Insecticides

Some metabolites with insecticidal action have been described. The famous B. thuringiensisproduces crystalline inclusion bodies consisting of delta-endotoxins (also referred to as Cry proteins) during sporulation. These proteins, which are formed by variable-molecular-weight polypeptides (27–140 kDa), are highly toxic for a broad range of pest insects [146]. P. fluorescensstrains exhibited a protective effect against aphids and some herbivorous beetles and termites [147]. The bacterium Lysinibacillus sphaericus(former Bacillus sphaericus) produces sphaericolysin, which is toxic for Spodoptera litura[148].

3.3.8 Induction of systemic response

Induced systemic resistance (ISR) is a term used for the resistance stimulated by chemicals agents or signals (elicitors) produced by beneficial microorganisms [149], whereby the plant’s innate defenses are potentiated against subsequent biotic challenges. In this way, the endophytes enhance the plant defenses against many pathogens [129]. The plant hormones jasmonic acid (JA) and ET are responsible for the regulation of the group of interrelated signaling pathways required to activate ISR. The main routes by which microbes regulate ISR in plants include: (i) phytohormones, (ii) pathogen-associated molecular patterns (PAMPs)/microbe-associated molecular patterns (MAMPs), and (iii) several elicitors (volatile organic compounds, siderophores, phytases, miRNAs, among others) [150]. Bacterial endophyte-mediated ISR has a broad spectrum of effectiveness. It was demonstrated that Acinetobacter, Azospirillum, Rhizobium, Pseudomonas, and Bacillusare beneficial inducers of systemic resistance in both leguminous and nonleguminous plants [151]. Dey et al. [91] described an endophytic isolate Klebsiella pneumoniaeHR1 from the root nodules of black mung bean (Vigna mungo) capable of reducing the occurrence of Macrophomina phaseolina, which is the causal agent of the root rot disease in Vigna. The lowest percentage of disease incidence (18.2%) was observed when K. pneumoniaewas applied in dual mode (seed bacterization + soil drench application). The increased activities of peroxidase (PR9), chitinase (PR3), and β-1,3-glucanase (PR2) in leaves indicated that K. pneumoniaeHR1 induces a systemic response.

Endophytic bacteria have diverse mechanisms that could contribute, even simultaneously, to protect the plant against the attack of different pathogens, having the potential to produce a more efficient pathogen control on the fields.

3.4 Abiotic stress tolerance

Under abiotic stress conditions (such as drought, salinity, flooding, heat, chilling, or heavy metals), several metabolic responses are shared among plant species. Most of the stresses cause photosynthesis inhibition, oxidative stress, and hormone imbalances ending in reductions of shoot growth and yield impairments [10, 97, 152, 153, 154]. In addition, some of the responses are interconnected, for instance, reactive oxygen species and hormones mutually affect each other at early and late phases of abiotic stress (reviewed by [155]).

Endophytic bacteria can protect the host plant against some of those deleterious effects, by at least two different ways (alone or combined): (i) activation of host stress response systems soon after exposure to stress (named induced systemic tolerance), and (ii) biosynthesis of chemicals, which will contribute to the stress tolerance in the host [9]. Here we focus on three mechanisms by which the bacteria can protect the plant host against abiotic stress: redox status, water balance, and hormone regulation.

3.4.1 Redox status regulation

Oxidative damage (caused by reactive oxygen and nitrogen species) is a common consequence of environmental stress, which may cause damage to lipids, proteins, and overall to any subcellular component [156]. Then, the activation of the enzymatic and nonenzymatic antioxidant system is critical to tolerate adverse conditions. Several endophytic bacteria mediate a higher induction of the antioxidant system under stress. For instance, under salinity, the inoculation of peanut with the halotolerant bacteria Brachybacterium saurashtrenseJG-06, Brevibacterium caseiJG-08, or HaererohalobacterJG-11 showed lower oxidative damage, ion leakage, and K/Na ratio and higher growth, IAA, and Ca [157], while the inoculation of B. subtilis(alone or combined with Mesorhizobium ciceri) of chickpea reduced hydrogen peroxide accumulation and improved plant growth [10]. Soybean plant inoculated with Curtobacteriumsp. SAK1 induced polyphenol oxidase activity, associated with growth protection and hormonal changes [158], while inoculated with Pseudomonas simiaeincreased catalase and peroxidase, but not polyphenol oxidase gene expression under salinity [159]. Also, soybean inoculated with B. cereus, Pseudomonas otitidis, and Pseudomonassp. showed a reduction of hydrogen peroxide and membrane oxidative damage caused by PEG-induced drought [160]. However, if these responses are generated by the plant or bacterial enzymes remains unknown.

3.4.2 Water use efficiency regulation

Under stress, plant tissues usually modulate osmotic and water retention, by stomata activity and/or accumulation of osmotically active compounds. The latter compounds, also known as compatible solutes, include sugars (e.g., sucrose, trehalose, etc.), organic acids (e.g., malate), inorganic ions (e.g., calcium), amino acids (e.g., glycine betaine, proline) [161]. An increase in drought tolerance was detected after the inoculation of Sphingomonassp. LK11 (isolated from Tephrosia apollinea) in soybean, by the accumulation of sugars and amino acids (glycine, glutamate, and proline) [162], and after the inoculation with Rhizobium etliin common bean, by the overexpression of trehalose-6-phosphate synthase [163]. Trehalose is an osmotically active compound that accumulates both in plants and microbes under stress. In particular, the role of trehalose in the tripartite symbiosis between plants, rhizobia, and arbuscular mycorrhiza under abiotic stress has been recently reviewed [164].

The optimal regulation of water use efficiency is critical to improved crop production. On one side is essential to survive dehydration stress (such as drought, salinity, heat, and chilling), but a constitutively highly efficient water use may reduce yields, by reducing CO2 assimilation. The use of bacteria that contribute to transiently intensify stress-tolerance responses can help to improve productivity in marginal environments. In addition, if the endophytic bacteria enhance the osmocompatible compounds in response to the stress, it is possible to increase not only the tolerance to drought, but also the tolerance to chilling, heat, and salinity stress, which share a “dehydration” component. In the latter case, we expect a partial tolerance due to the ion toxicity, not related to the reduction in water potential.

3.4.3 Hormone regulation

As it was mentioned before, endophytic bacteria can regulate hormone synthesis and degradation and synthesize some of the plant hormone-like compounds by themselves. In addition, specific hormone regulation could also protect against abiotic stress increasing growth, yield, and survival.

Abscisic acid (ABA) is the main plant hormone related to water stress. It stimulates root growth and optimizes water uptake and nutrient acquisition, regulates shoot and root hydraulic conductivity, and upregulates the antioxidant system and compatible osmolytes synthesis [161]. The inoculation of Sphingomonasin soybean leaves induced ABA accumulation and reduced chlorophyll degradation and growth inhibition. However, under drought, ABA levels were lower in inoculated plants. So, in this case, the initial increase of ABA might have a role in acclimation to the stress induced by the bacteria inoculation [162]. In addition, ABA may interfere with SA-, JA-, and ET-mediated plant defenses [165], which may have undesired consequences under biotic stress.

Ethylene (ET) is usually considered a plant growth inhibitor, but at low levels, it can promote growth in several plant species. At moderate levels, ET inhibits both root and shoots elongation, while at high levels, enhances senescence and organ abscission [166]. The direct precursor of ET in the plant biosynthetic pathway, 1-aminocyclopropane-1-carboxylate (ACC), is exuded from plant roots together with other amino acids. The enzyme ACC deaminase cleaves ACC into ammonia and alfa-ketobutyrate. Plant growth promoter bacteria that express the enzyme ACC deaminase utilize their products (ammonia and ketobutyrate) as nitrogen and carbon sources, respectively. Bacterial ACC deaminase is not excreted from the bacterial cytoplasm [167]; hence, the decrease of plant ET levels relies on the ability of ACC deaminase expressing bacteria to take up ACC before it is oxidized by the plant’s ACC oxidase [167]. When those bacteria are present, ET production could be lowered, relieving stress-induced growth inhibition [168]. For instance, the inoculation of pea (P. vulgaris) plants with Aneurinibacillus aneurinilyticusand Paenibacillussp., two strains with high ACC activity in vitro, increased salt and drought tolerance. The combined inoculation reduced plant ET content and increased root and shoot length and biomass, as well as chlorophyll content [169]. The inoculation of alfalfa plants with Bacillus megateriumNMp082, which can produce ACC deaminase activity and IAA in vitro, also enhanced their salt tolerance [170]. Lastly, a novel mechanism was proposed in which salt tolerance is mediated by the activation of ET signaling. The inoculation of alfalfa with the bacteria Enterobactersp. SA187 (isolated from a desert plant) increases salt tolerance, and studies in Arabidopsis indicate that the bacteria activate the ET signaling pathway [171]. The different mechanisms by which microorganisms can interfere with ET signaling were reviewed by Ravanbakhsh et al. [167].

Auxins regulate many important physiological processes related to growth and development affecting photosynthesis and responses to stress [161]. Under stress, auxins stimulate root elongation and density, increasing the water and nutrient availability, although they may interfere with SA-dependent plant defenses.

The inoculation of chickpea with Serratiasp. in nutrient-deficient soil induced more IAA and higher yields [172], while the same plant inoculated with IAA-producing B. subtilisNUU4 in combination with M. ciceriIC53 stimulated root and shoot biomass and improved nodule formation under salt stress [173]. Soybean plants inoculated with B. aryabhattaistrain SRB02, which produces IAA, GA, and ABA, showed higher drought tolerance through stomatal closure, and higher root and shoot rates under high temperatures [116], and the same host treated with Sphingomonassp. LK11 and Serratia marcescensTP1 (which produced IAA in vitro) stimulated root and shoot growth with increased ABA and GA and reduction of JA [162]. Overall, abiotic stress protection mediated by plant hormones and crop salinity protection mediated by beneficial bacteria have been reviewed [10, 174, 175].

Some primary stresses share the responses among them, such as those that generate dehydration (water or temperature deficit) or oxidative stress (dehydration, hypoxia, ions). For example, the double inoculation of chickpea with M. ciceriIC53 and B. subtilisNUU4 reduced the infection rate of root rot caused by Fusarium solaniin salty soils [173], although the mechanism was not determined. Then, a bacteria strain, inducing a protective mechanism against oxidative stress, can protect the crop against a diversity of stress, which generates redox imbalances. Consequently, knowing the responses that each stress triggers in the plant may allow us to predict which bacteria or group of them could protect the plant against a combination of stresses.

Advertisement

4. Synthetic communities of plant-associated bacteria to a more sustainable agriculture

Natural microbial communities within the plants are complex systems, with unknown functions and interrelationships among the microbial species and with the host plant. Small consortia of bacteria, with a “designed” composition, called “synthetic communities,” reduce the complexity of those systems to be studied and used. The goal is to simplify the network while preserving the interactions and most of the functions, which may be lost in single plant-microbe interactions [175]. The use of synthetic communities allow us to ask questions about the performance and stability of the microbial community as well as to study conditions necessary to generate interaction patterns required to provide specific benefits. They are not only valuable as models but also as assays for biotechnological approaches [176].

4.1 How to study synthetic communities?

Manipulative experiments with synthetic bacterial communities can validate the predicted keystone species and, in general, help to find out specific effects of the resulting community under some pathogen infection or environmental condition. Those studies required in vitroexperiments in gnotobiotic (germ-free) systems [11], where the plant is inoculated with a few or several microbial species, and the diversity is monitored across time. For instance, a gnotobiotic system was used to study the bacteria-colonizing alfalfa nodules [131]. The authors inoculate alfalfa with the four accessory bacterial members B. brevisAg35, Paenibacillussp. Ag47, Pseudomonassp. Ag54, and Pantoea agglomeransAg15, plus the nodulating strain Sinorhizobium melilotiRM1021. They observed that the addition of B. brevisneutralized the cooperation between Pseudomonassp. Ag54 and Paenibacillussp. Ag47, shifting the community from cooperative to competitive.

Another alternative, it is to use synthetic communities in a non-germ-free environment (more accessible and simpler to set up) to evaluate the protective or antagonist effect of a small group of species under a particular condition. Overall, only a few studies of the kind have been carried out in legumes until now. For instance, Lu et al. [177] described the diversity of nonrhizobial bacteria (32 genera) in legume nodules inoculated with Bradyrhizobium elkaniiH255, Rhizobium multihospitium–like HT221, or Burkholderia pyrrociniawith or without the addition of N fertilization. The study suggested a vital role of that group of bacteria in N fixation in legumes.

The synthetic communities are a way to understand how microbial communities are built in the plants but also the base to a more complex (and likely more effective) phytostimulation effects, biological control of diseases, and protection against abiotic stress.

4.2 Can we manipulate the plant microbiome to improve the fitness or yield of legumes?

There are a variety of strategies to manipulate the microbiome of a plant host and could be classified according to the direct target: (i) the microbiome itself, (ii) the plant genome, or (iii) the holobiome (plant plus microbial community) (reviewed by [39, 178]).

The microbiome (i) can be modified by the exogenous inoculation of the microbe, increasing the abundance of a single strain or a few species together. The first case is the most traditionally used, and there are thousands of examples, such as the inoculation with rhizobia. In those cases, the single strain should be compatible with the host genotype and able to overcome the competence of the native microbiome and the environmental conditions. The second case is open to unexplored scenarios, such as an infinite possibility of a higher number of strains/species combinations. This strategy is just starting to be explored, such as with non-nodulating bacterial species present in the nodules (and sometimes in the rest of the plant) that promote nodulation. For instance, the inoculation of common bean (P. vulgarisL.) with Paenibacillus polymyxaand B. megateriumstrains showed a synergistic effect with Rhizobiumstrains on the plant growth [179]. On the contrary, the inoculation of alfalfa with different strains of the mutualistic P. fluorescens, showed that the increase in the community richness led to a negative complementary effect causing the loss of the protective effect against pathogens [180]. These results highlight the importance to evaluate the effects of any agricultural treatment or management on the microbial community.

The inoculation with synthetic communities has the advantage (over the use of the native microbiome) to allow the design of a community, which includes distant species (which may provide complementary benefits), or similar species, which increase the efficiency of the community (by using a wider diversity of resources) [19]. However, with the number and diversity of species, it also increases the complexity to handle the system and to commercialize the inoculants.

The plant genome (ii) could be manipulated by traditional breeding, gene editing, or transgenesis, changing the ability of the host to interact with the microbes (such as changing the exudates or volatiles). Instead of only breeding for pathogen resistance or abiotic stress tolerance, this could be a complementary alternative to select crop legumes to be more responsive to the presence of beneficial microbes [181]. For instance, modern accessions of common bean showed a lower abundance of Bacteroidetes and higher of Actinobacteria and Proteobacteria than the wild accession [79], with a gain in the diversity of rhizospheric bacterial and a stronger effect of the bean genotype [182]. In addition, Mendes et al. [183] showed that common bean breeding for Fusarium oxysporumresistance altered the functionality of the rhizosphere, unintentionally increasing the host protection against other pathogens. We hypothesize that a similar effect is happening in the endosphere, although it has not been explored yet. Additionally, when using this approach, it is relevant to evaluate that host defenses against pathogens are still functional.

Lastly, the holobiome (iii) could be altered through specific agricultural practices such as crop rotation, mineral, and organic fertilization, tillage practices, etc., favoring a specific community composition or function. Several studies reported the effect of agricultural management on the rhizosphere of legumes and its effect on crop performance. A meta-study showed the effect of crop rotation, intercropping, or companion planting on the rhizospheric microbial richness and diversity [184]. Those agricultural practices did not always have positive effects in richness and diversity, and legume-cereal crop rotation (relevant to reduce N fertilization) showed inconsistent results on the microbiome. A recent study showed that pea-wheat rotations showed no effect in the diversity index, but they affected the specific co-occurrence networks for each crop [185] suggesting a more complex effect of crop rotation that needs to be further studied. Certain chickpea cultivars select a more beneficial microbiome for the subsequent wheat plants, and they were associated with the antagonist species Penicillium canescens[186]. Red clover and potato crops in rotation shared 73% of the bacterial endophytes, and 21% of those species promoted plant growth and yield in potato bioassays [187], while 74% of the shared species showed some degree of in vitroantibiosis against Rhizoctonia solani, a pathogen of both crops. We hypothesize that changing the rhizosphere will affect the endosphere too, by changing the available microbial pool, but that effect has not been explored at legume endophytic microbiomes.

4.3 Are there collateral impacts of using synthetic communities in agriculture?

Lastly, it is important to consider alive microbes will be released to the environment and into products used or consumed by humans and animals, so the potential risks need to be considered and tested [188]. There is no internationally agreed protocol to be complimented, but recently, Vilchez et al. [189] have proposed an Environmental and Human Safety Index (EHSI) protocol to determine the safety of the bacterial strains. The protocol evaluates microbial and animal sensitivity/pathogenicity and ecotoxicity in different model organisms, and it has been validated for many well-known bacteria. In addition, on the agronomical level, little information is available on the nontarget effects on microbial communities and the resulting impact on the soil function [32].

Advertisement

5. Final remarks and future directions

Agricultural legume crops are usually treated with synthetic chemicals to increase growth, control diseases, and mitigate environmental stress, which has high economic, environmental, and health costs. However, there is a myriad of endophytic bacteria that colonize the plant at least in part of its life cycle that could replace or complement those chemicals with great benefits for the plants. In addition, the huge bacterial diversity could be combined to provide several benefits at the same time. For that purpose, the use of synthetic communities is critical to study how the microbial community evolves within the plant as much as their beneficial effects.

The use of synthetic bacterial communities to improve and make more sustainable legume production is still in early stages of development, but it is a promising field. Using synthetic communities has the theoretical advantage of combining strain benefits and contributing to the survival of the bacteria on the field and inside the plant while producing a package of benefits for the legume. Although it is expected to have more difficulties at the time of commercial production.

On the other hand, changes in the agricultural management with some specific purpose could be a more affordable strategy for most of the small-scale producers in low-income countries, which are the ones in more need of sustainable and accessible technologies. Additionally, the use of soil-native microorganisms could have the advantage to reduce possible adverse consequences on the environment and health.

For the moment, the knowledge about endophytic bacteria in legumes, the possibility to “design” synthetic communities for a specific goal, and to manipulate the holobiome by agricultural practices is still incipient. However, the potential benefits for current agriculture to improve yields and sustainability have a great unexplored potential in the endophytic bacterial microbiome of legume crops.

Advertisement

Acknowledgments

This work was supported by FONCyT (PICT STARTUP 2018-0065, PICT 2018-01326) and INTA (I069, I127, I516). CC is a CONICET fellow. MIM and TT are Career Investigators of CONICET. MIM, LV, and MCG are Career Investigators of INTA.

Advertisement

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Advertisement

Author contributions

LV and MM conceived and planned the overall idea of the review manuscript. All authors contributed to the article and approved the submitted version.

References

  1. 1. Hallmann J, Quadt-Hallmann A, Mahaffee WF, Kloepper JW. Bacterial endophytes in agricultural crops. Canadian Journal of Microbiology. 1997;43:895-914
  2. 2. Santoyo G, Moreno-Hagelsieb G, del Carmen Orozco-Mosqueda M, Glick BR. Plant growth-promoting bacterial endophytes. Microbiological Research. 2016;183:92-99
  3. 3. Dudeja SS, Giri R, Saini R, Suneja-Madan P, Kothe E. Interaction of endophytic microbes with legumes. Journal of Basic Microbiology. 2012;52:248-260
  4. 4. Ek-Ramos MJ, Gomez-Flores R, Orozco-Flores AA, Rodríguez-Padilla C, González-Ochoa G, Tamez-Guerra P. Bioactive products from plant-endophytic Gram-positive bacteria. Frontiers in Microbiology. 2019;10:463
  5. 5. Gray EJ, Smith DL. Intracellular and extracellular PGPR: commonalities and distinctions in the plant–bacterium signaling processes. Soil Biology and Biochemistry. 2005;37:395-412
  6. 6. Sugiyama A, Ueda Y, Zushi T, Takase H, Yazaki K. Changes in the bacterial community of soybean rhizospheres during growth in the field. PLoS ONE. 2014;9:e100709
  7. 7. Thomas P, Franco CMM. Intracellular bacteria in plants: Elucidation of abundant and diverse cytoplasmic bacteria in healthy plant cells using in vitro cell and callus cultures. Microorganisms. 2021;9:269
  8. 8. Naveed M, Aziz MZ, Yaseen M. Perspectives of using endophytic microbes for legume improvement. In: Zaidi A, Khan MS, Musarrat J, editors. Microbes for Legume Improvement. Switzerland: Springer International Publishing; 2017. pp. 277-299
  9. 9. Lata R, Chowdhury S, Gond SK, White JF. Induction of abiotic stress tolerance in plants by endophytic microbes. Letters in Applied Microbiology. 2018;66:268-276
  10. 10. Egamberdieva D, Wirth SJ, Alqarawi AA, Abd-Allah EF, Hashem A. Phytohormones and beneficial microbes: Essential components for plants to balance stress and fitness. Frontiers in Microbiology. 2017;8:2104
  11. 11. Trivedi P, Leach JE, Tringe SG, Sa T, Singh BK. Plant–microbiome interactions: from community assembly to plant health. Nature Reviews Microbiology. 2020;18:607-621
  12. 12. Kawasaki A, Donn S, Ryan PR, Mathesius U, Devilla R, Jones A, et al. Microbiome and exudates of the root and rhizosphere of Brachypodium distachyon, a model for wheat. PLoS ONE. 2016;11:e0164533
  13. 13. Pétriacq P, Williams A, Cotton A, McFarlane AE, Rolfe SA, Ton J. Metabolite profiling of non-sterile rhizosphere soil. The Plant Journal. 2017;92:147-162
  14. 14. Prieto P, Schilirò E, Maldonado-González MM, Valderrama R, Barroso-Albarracín JB, Mercado-Blanco J. Root hairs play a key role in the endophytic colonization of olive roots by Pseudomonas spp. with biocontrol activity. Microbial Ecology. 2011;62:435-445
  15. 15. Senthilkumar M, Anandham R, Madhaiyan M, Venkateswaran V, Sa T. Endophytic bacteria: Perspectives and applications in agricultural crop production. In: Maheshwari DK, editor. Bacteria in Agrobiology: Crop Ecosystems. Berlin, Heidelberg: Springer; 2011. pp. 61-96
  16. 16. Afzal I, Shinwari ZK, Sikandar S, Shahzad S. Plant beneficial endophytic bacteria: Mechanisms, diversity, host range and genetic determinants. Microbiological Research. 2019;221:36-49
  17. 17. Carvalho TLG, Balsemão-Pires E, Saraiva RM, Ferreira PCG, Hemerly AS. Nitrogen signalling in plant interactions with associative and endophytic diazotrophic bacteria. Journal of Experimental Botany. 2014;65:5631-5642
  18. 18. Agler MT, Ruhe J, Kroll S, Morhenn C, Kim S-T, Weigel D, et al. Microbial hub taxa link host and abiotic factors to plant microbiome variation. PLoS Biology. 2016;14:e1002352
  19. 19. Pascale A, Proietti S, Pantelides IS, Stringlis IA. Modulation of the root microbiome by plant molecules: The basis for targeted disease suppression and plant growth promotion. Frontiers in Plant Science. 2020;10:1741
  20. 20. Sasse J, Martinoia E, Northen T. Feed your friends: Do plant exudates shape the root microbiome? Trends in Plant Science. 2018;23:25-41
  21. 21. Kwak M-J, Kong HG, Choi K, Kwon S-K, Song JY, Lee J, et al. Rhizosphere microbiome structure alters to enable wilt resistance in tomato. Nature Biotechnology. 2018;36:1100-1109
  22. 22. Mendes LW, Raaijmakers JM, de Hollander M, Mendes R, Tsai SM. Influence of resistance breeding in common bean on rhizosphere microbiome composition and function. The ISME Journal. 2018;12:212-224
  23. 23. Plett JM, Martin FM. Know your enemy, embrace your friend: Using omics to understand how plants respond differently to pathogenic and mutualistic microorganisms. The Plant Journal. 2018;93:729-746
  24. 24. Mengistu AA. Endophytes: Colonization, behaviour, and their role in defense mechanism. International Journal of Microbiology. 2020;2020:e6927219
  25. 25. Oukala N, Aissat K, Pastor V. Bacterial endophytes: The hidden actor in plant immune responses against biotic stress. Plants (Basel). 2021;10:1012
  26. 26. Deng Q, Aras S, Yu C-L, Dzantor EK, Fay PA, Luo Y, et al. Effects of precipitation changes on aboveground net primary production and soil respiration in a switchgrass field. Agriculture, Ecosystems & Environment. 2017;248:29-37
  27. 27. Alquéres S, Meneses C, Rouws L, Rothballer M, Baldani I, Schmid M, et al. The bacterial superoxide dismutase and glutathione reductase are crucial for endophytic colonization of rice roots by Gluconacetobacter diazotrophicus PAL5. Molecular Plant-Microbe Interactions. 2013;26:937-945
  28. 28. Jiménez-Guerrero I, Pérez-Montaño F, Monreal JA, Preston GM, Fones H, Vioque B, et al. The Sinorhizobium (Ensifer) fredii HH103 Type 3 secretion system suppresses early defense responses to effectively nodulate soybean. Molecular Plant-Microbe Interactions. 2015;28:790-799
  29. 29. Frank B. Ueber die pilzsymbiose der leguminosen. Berichte der Deutschen Botanischen Gesellschaft. 1889;7:332-346
  30. 30. Peix A, Ramírez-Bahena MH, Velázquez E, Bedmar EJ. Bacterial associations with legumes. Critical Reviews in Plant Sciences. 2015;34:17-42
  31. 31. De Meyer SE, De Beuf K, Vekeman B, Willems A. A large diversity of non-rhizobial endophytes found in legume root nodules in Flanders (Belgium). Soil Biology and Biochemistry. 2015;83:1-11
  32. 32. Tsiknia M, Tsikou D, Papadopoulou KK, Ehaliotis C. Multi-species relationships in legume roots: From pairwise legume-symbiont interactions to the plant – microbiome – soil continuum. FEMS Microbiology Ecology. 2021;97:fiaa222
  33. 33. Angelini J, Ibáñez F, Taurian T, Tonelli ML, Valetti L, Fabra A. A study on the prevalence of bacteria that occupy nodules within single peanut plants. Current Microbiology. 2011;62:1752-1759
  34. 34. Hoque MS, Broadhurst LM, Thrall PH. Genetic characterization of root-nodule bacteria associated withAcacia salicinaandA. stenophylla(Mimosaceae) across southeastern Australia. International Journal of Systematic and Evolutionary Microbiology. 2011;61:299-309
  35. 35. Vílchez JI, Lally RD, Morcillo RJL. Biosafety evaluation: a necessary process ensuring the equitable beneficial effects of PGPR. In: Advances in PGPR Research. Wallingford, UK: CABI; 2017. pp. 50-74
  36. 36. Huang Y, Kuang Z, Deng Z, Zhang R, Cao L. Endophytic bacterial and fungal communities transmitted from cotyledons and germs in peanut (Arachishypogaea L.) sprouts. Environmental Science and Pollution Research. 2017;24:16458-16464
  37. 37. Li S, Tian Y, Wu K, Ye Y, Yu J, Zhang J, et al. Modulating plant growth–metabolism coordination for sustainable agriculture. Nature. 2018;560:595-600
  38. 38. Alok D, Annapragada H, Singh S, Murugesan S, Singh NP. Symbiotic nitrogen fixation and endophytic bacterial community structure in Bt-transgenic chickpea (Cicer arietinumL). Scientific Reports. 2020;10:5453
  39. 39. Lu J, Yang F, Wang S, Ma H, Liang J, Chen Y. Co-existence of rhizobia and diverse non-rhizobial bacteria in the rhizosphere and nodules of dalbergia odorifera seedlings inoculated withBradyrhizobium elkanii,Rhizobium multihospitium–like andBurkholderia pyrrocinia–like strains. Frontiers in Microbiology. 2017;8:2255
  40. 40. Zheng Y, Liang J, Zhao D-L, Meng C, Xu Z-C, Xie Z-H, et al. The root nodule microbiome of cultivated and wild halophytic legumes showed similar diversity but distinct community structure in yellow river delta saline soils. Microorganisms. 2020;8:207
  41. 41. Rascovan N, Carbonetto B, Perrig D, Díaz M, Canciani W, Abalo M, et al. Integrated analysis of root microbiomes of soybean and wheat from agricultural fields. Scientific Reports. 2016;6:28084
  42. 42. Liu F, Rice JH, Lopes V, Grewal P, Lebeis SL, Hewezi T, et al. Overexpression of strigolactone-associated genes exerts fine-tuning selection on soybean rhizosphere bacterial and fungal microbiome. Phytobiomes Journal. 2020;4:239-251
  43. 43. Xiao X, Chen W, Zong L, Yang J, Jiao S, Lin Y, et al. Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments. Molecular Ecology. 2017;26:1641-1651
  44. 44. Hansen BL, Pessotti R d C, Fischer MS, Collins A, El-Hifnawi L, Liu MD, et al. Cooperation, competition, and specialized metabolism in a simplified root nodule microbiome. MBio. 2020;11:e01917-e01920
  45. 45. Wigley K, Moot D, Wakelin SA, Laugraud A, Blond C, Seth K, et al. Diverse bacterial taxa inhabit root nodules of lucerne (Medicago sativaL.) in New Zealand pastoral soils. Plant and Soil. 2017;420:253-262
  46. 46. Brown SP, Grillo MA, Podowski JC, Heath KD. Soil origin and plant genotype structure distinct microbiome compartments in the model legumeMedicago truncatula. Microbiome. 2020;8:139
  47. 47. Lv X, Wang Q, Zhang X, Hao J, Li L, Chen W, et al. The temporal structure and association networks of endophytic bacteria in pea roots and nodules. Research Square. 2021
  48. 48. Raja P, Rangasamy A, Gopal NO, Meena S. Isolation and characterization of nodule endophytes from bunching and semi-spreading groundnut genotypes. The Madras Agricultural Journal. 2019;106:388-394
  49. 49. Geetha Thanuja K, Annadurai B, Thankappan S, Uthandi S. Non-rhizobial endophytic (NRE) yeasts assist nodulation of Rhizobium in root nodules of blackgram (Vigna mungoL.). Archives of Microbiology. 2020;202:2739-2749
  50. 50. Bhutani N, Maheshwari R, Negi M, Suneja P. Optimization of IAA production by endophytic Bacillus spp. from Vigna radiata for their potential use as plant growth promoters. Israel Journal of Plant Sciences. 2018;65:83-96
  51. 51. Muindi MM, Muthini M, Njeru EM, Maingi J. Symbiotic efficiency and genetic characterization of rhizobia and non rhizobial endophytes associated with cowpea grown in semi-arid tropics of Kenya. Heliyon. 2021;7:e06867
  52. 52. Hartman K, van der Heijden MG, Roussely-Provent V, Walser J-C, Schlaeppi K. Deciphering composition and function of the root microbiome of a legume plant. Microbiome. 2017;5:2
  53. 53. Cordero J, de Freitas JR, Germida JJ. Bacterial microbiome associated with the rhizosphere and root interior of crops in Saskatchewan, Canada. Canadian Journal of Microbiology. 2020;66:71-85
  54. 54. Dhole A, Shelat H, Vyas R, Jhala Y, Bhange M. Endophytic occupation of legume root nodules by nifH-positive non-rhizobial bacteria, and their efficacy in the groundnut (Arachis hypogaea). Annales de Microbiologie. 2016;66:1397-1407
  55. 55. Dai Y, Li X, Wang Y, Li C, He Y, Lin H, et al. The differences and overlaps in the seedresident microbiome of four Leguminous and three Gramineous forages. Microbial Biotechnology. 2020;13:1461-1476
  56. 56. Preyanga R, Anandham R, Krishnamoorthy R, Senthilkumar M, Gopal NO, Vellaikumar A, et al. Groundnut (Arachis hypogaea) nodule Rhizobium and passenger endophytic bacterial cultivable diversity and their impact on plant growth promotion. Rhizosphere. 2021;17:100309
  57. 57. Archana T, Rajendran L, Manoranjitham SK, Santhana Krishnan VP, Paramasivan M, Karthikeyan G. Culture-dependent analysis of seed bacterial endophyte, Pseudomonas spp. EGN 1 against the stem rot disease (Sclerotium rolfsiiSacc.) in groundnut. Egyptian Journal of Biological Pest Control. 2020;30:119
  58. 58. Brígido C, Singh S, Menéndez E, Tavares MJ, Glick BR, Félix M d R, et al. Diversity and functionality of culturable endophytic bacterial communities in chickpea plants. Plants (Basel). 2019;8:42
  59. 59. Vo QAT, Ballard RA, Barnett SJ, Franco CMM. Isolation and characterisation of endophytic actinobacteria and their effect on the growth and nodulation of chickpea (Cicer arietinum). Plant and Soil. 2021;466:357-371
  60. 60. Renu V, Kumar A, Annapragada H, Singh Y, Senthil-Kumar M. Identification and characterization of root nodule associated bacteria from chickpea germplasm lines-Indian Journals. Journal of Food Legumes. 2018;31:215-220
  61. 61. Zhao L, Xu Y, Lai X. Antagonistic endophytic bacteria associated with nodules of soybean (Glycine maxL.) and plant growth-promoting properties. Journal of Microbiology. 2017;49:269-278
  62. 62. de Almeida Lopes KB, Carpentieri-Pipolo V, Oro TH, Stefani Pagliosa E, Degrassi G. Culturable endophytic bacterial communities associated with field-grown soybean. Journal of Applied Microbiology. 2016;120:740-755
  63. 63. Kumawat KC, Sharma P, Sirari A, Singh I, Gill BS, Singh U, et al. Synergism ofPseudomonas aeruginosa(LSE-2) nodule endophyte with Bradyrhizobium sp. (LSBR-3) for improving plant growth, nutrient acquisition and soil health in soybean. World Journal of Microbiology and Biotechnology. 2019;35:47
  64. 64. Rasheed M, Naseer T, Hassan A, ul Hassan F, Hayat R, Jilani G, et al. Isolation of nodule associated bacteria for promotion of lentil growth. PJAR. 2020:33
  65. 65. Sendi Y, Pfeiffer T, Koch E, Mhadhbi H, Mrabet M. Potential of common bean (Phaseolus vulgarisL.) root microbiome in the biocontrol of root rot disease and traits of performance. Journal of Plant Diseases and Protection. 2020;127:453-462
  66. 66. Maheshwari R, Bhutani N, Bhardwaj A, Suneja P. Functional diversity of cultivable endophytes fromCicer arietinumandPisum sativum: Bioprospecting their plant growth potential. Biocatalysis and Agricultural Biotechnology. 2019;20:101229
  67. 67. Aserse AA, Räsänen LA, Aseffa F, Hailemariam A, Lindström K. Diversity of sporadic symbionts and nonsymbiotic endophytic bacteria isolated from nodules of woody, shrub, and food legumes in Ethiopia. Applied Microbiology and Biotechnology. 2013;97:10117-10134
  68. 68. Vendan RT, Balachandar D. Assessing the plant growth-promoting traits and host specificity of endophytic bacteria of pulse crops. LR. 2021;LR-4491:1-10
  69. 69. Missbah El Idrissi M, Lamin H, Bouhnik O, Lamrabet M, Alami S, Jabrone Y, et al. Characterization ofPisum sativumandVicia fabamicrosymbionts in Morocco and definition of symbiovar viciae in Rhizobium acidisoli. Systematic and Applied Microbiology. 2020;43:126084
  70. 70. Brígido C, Menéndez E, Paço A, Glick BR, Belo A, Félix MR, et al. Mediterranean native leguminous plants: A reservoir of endophytic bacteria with potential to enhance chickpea growth under stress conditions. Microorganisms. 2019;7:392
  71. 71. Vandenkoornhuyse P, Quaiser A, Duhamel M, Van AL, Dufresne A. The importance of the microbiome of the plant holobiont. New Phytologist. 2015;206:1196-1206
  72. 72. Papik J, Folkmanova M, Polivkova-Majorova M, Suman J, Uhlik O. The invisible life inside plants: Deciphering the riddles of endophytic bacterial diversity. Biotechnology Advances. 2020;44:107614
  73. 73. Frank AC, Saldierna Guzmán JP, Shay JE. Transmission of bacterial endophytes. Microorganisms. 2017;5:70
  74. 74. Ding T, Palmer MW, Melcher U. Community terminal restriction fragment length polymorphisms reveal insights into the diversity and dynamics of leaf endophytic bacteria. BMC Microbiology. 2013;13:1
  75. 75. Alain K, Querellou J. Cultivating the uncultured: Limits, advances and future challenges. Extremophiles. 2009;13:583-594
  76. 76. Allan E. Metagenomics: unrestricted access to microbial communities. Virulence. 2014;5:397-398
  77. 77. Lucaciu R, Pelikan C, Gerner SM, Zioutis C, Köstlbacher S, Marx H, et al. A bioinformatics guide to plant microbiome analysis. Frontiers in Plant Science. 2019;10:1313
  78. 78. Yeoh YK, Dennis PG, Paungfoo-Lonhienne C, Weber L, Brackin R, Ragan MA, et al. Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence. Nature Communications. 2017;8:215
  79. 79. Pérez-Jaramillo JE, Carrión VJ, Bosse M, Ferrão LFV, de Hollander M, Garcia AAF, et al. Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits. The ISME Journal. 2017;11:2244-2257
  80. 80. Banerjee S, Schlaeppi K, van der Heijden MGA. Keystone taxa as drivers of microbiome structure and functioning. Nature Reviews. Microbiology. 2018;16:567-576
  81. 81. van der Heijden MGA, Hartmann M. Networking in the plant microbiome. PLoS Biology. 2016;14(2):e1002378
  82. 82. Jones P, Garcia BJ, Furches A, Tuskan GA, Jacobson D. Plant host-associated mechanisms for microbial selection. Frontiers in Plant Science. 2019;10:862
  83. 83. Sharma M, Sudheer S, Usmani Z, Rani R, Gupta P. Deciphering the omics of plant-microbe interaction: Perspectives and new insights. Current Genomics. 2020;21:343-362
  84. 84. Xu L, Pierroz G, Wipf HM-L, Gao C, Taylor JW, Lemaux PG, et al. Holo-omics for deciphering plant-microbiome interactions. Microbiome. 2021;9:69
  85. 85. Chaudhary T, Gera R, Shukla P. Emerging molecular tools for engineering phytomicrobiome. Indian Journal of Microbiology. 2021;61:116-124
  86. 86. Lugtenberg B, Kamilova F. Plant-growth-promoting rhizobacteria. Annual Review of Microbiology. 2009;63:541-556
  87. 87. Gourion B, Berrabah F, Ratet P, Stacey G. Rhizobium-legume symbioses: The crucial role of plant immunity. Trends in Plant Science. 2015;20:186-194
  88. 88. Taurian T, Aguilar OM, Fabra A. Characterization of nodulating peanut rhizobia isolated from a native soil population in Córdoba, Argentina. Symbiosis. 2002;33:59-72
  89. 89. Anzuay MS, Ludueña LM, Angelini JG, Fabra A, Taurian T. Beneficial effects of native phosphate solubilizing bacteria on peanut (Arachis hypogaeaL) growth and phosphorus acquisition. Symbiosis. 2015;66:89-97
  90. 90. Taurian T, Ibáñez F, Angelini J, Tonelli ML, Fabra A. Endophytic bacteria and their role in legumes growth promotion. In: Maheshwari DK, editor. Bacteria in Agrobiology: Plant Probiotics. Berlin, Heidelberg: Springer; 2012. pp. 141-168
  91. 91. Dey AK, Sharma M, Meshram MR. An analysis of leaf chlorophyll measurement method using chlorophyll meter and image processing technique. Procedia Computer Science. 2016;85:286-292
  92. 92. Podile AR, Kishore GK. Plant growth-promoting rhizobacteria. In: Gnanamanickam SS, editor. Plant-Associated Bacteria. Dordrecht: Springer Netherlands; 2006. pp. 195-230
  93. 93. Rodríguez H, Fraga R, Gonzalez T, Bashan Y. Genetics of phosphate solubilization and its potential applications for improving plant growth-promoting bacteria. Plant and Soil. 2006;287:15-21
  94. 94. Anzuay MS, Ciancio MGR, Ludueña LM, Angelini JG, Barros G, Pastor N, et al. Growth promotion of peanut (Arachis hypogaeaL.) and maize (Zea maysL.) plants by single and mixed cultures of efficient phosphate solubilizing bacteria that are tolerant to abiotic stress and pesticides. Microbiological Research. 2017;199:98-109
  95. 95. Lucero CT, Lorda GS, Anzuay MS, Ludueña LM, Taurian T. Peanut endophytic phosphate solubilizing bacteria increase growth and P content of soybean and maize plants. Current Microbiology. 2021;78:1961-1972
  96. 96. Oteino N, Lally RD, Kiwanuka S, Lloyd A, Ryan D, Germaine KJ, et al. Plant growth promotion induced by phosphate solubilizing endophytic Pseudomonas isolates. Frontiers in Microbiology. 2015;6:745
  97. 97. Yadav AN. Biodiversity and biotechnological applications of host-specific endophytic fungi for sustainable agriculture and allied sectors. Acta Scientific Microbiology. 2018;1:1-5
  98. 98. Valetti L, Iriarte L, Fabra A. Growth promotion of rapeseed (Brassica napus) associated with the inoculation of phosphate solubilizing bacteria. Applied Soil Ecology. 2018;132:1-10
  99. 99. Choi O, Kim J, Kim J-G, Jeong Y, Moon JS, Park CS, et al. Pyrroloquinoline quinone is a plant growth promotion factor produced by Pseudomonas fluorescens B16. Plant Physiology. 2008;146:657-668
  100. 100. Ahmed N, Shahab S. Involvement of bacterial pyrroloquinoline in plant growth promotion: A novel discovery. World Applied Sciences Journal. 2010;8:57-61
  101. 101. Ludueña LM, Anzuay MS, Angelini JG, Barros G, Luna MF, Monge M d P, et al. Role of bacterial pyrroloquinoline quinone in phosphate solubilizing ability and in plant growth promotion on strain Serratia sp. S119. Symbiosis. 2017;72:31-43
  102. 102. Verma J, Yadav J, Tiwari K, Lavakush SV. Impact of plant growth promoting rhizobacteria on crop production. International Journal of Agricultural Research. 2010;5:954-983
  103. 103. Carvalhais LC, Dennis PG, Badri DV, Tyson GW, Vivanco JM, Schenk PM. Activation of the jasmonic acid plant defence pathway alters the composition of rhizosphere bacterial communities. PLoS ONE. 2013;8:e56457
  104. 104. Fadiji AE, Babalola OO. Elucidating mechanisms of endophytes used in plant protection and other bioactivities with multifunctional prospects. Frontiers in Bioengineering and Biotechnology. 2020;8:467
  105. 105. Kraepiel AML, Bellenger JP, Wichard T, Morel FMM. Multiple roles of siderophores in free-living nitrogen-fixing bacteria. Biometals. 2009;22:573-581
  106. 106. Taurian T, Anzuay MS, Angelini JG, Tonelli ML, Ludueña L, Pena D, et al. Phosphatesolubilizing peanut associated bacteria: Screening for plant growth-promoting activities. Plant and Soil. 2010;329:421-431
  107. 107. He X, Han G, Lin Y, Tian X, Xiang C, Tian Q, et al. Diversity and decomposition potential of endophytes in leaves of aCinnamomum camphoraplantation in China. Ecological Research. 2012;27:273-284
  108. 108. Eichmann R, Richards L, Schäfer P. Hormones as go-betweens in plant microbiome assembly. The Plant Journal. 2021;105:518-541
  109. 109. Liu H, Carvalhais LC, Crawford M, Singh E, Dennis PG, Pieterse CMJ, et al. Inner plant values: Diversity, colonization and benefits from endophytic bacteria. Frontiers in Microbiology. 2017;8:2552
  110. 110. Casanova-Sáez R, Mateo-Bonmatí E, Ljung K. Auxin metabolism in plants. Cold Spring Harbor Perspectives in Biology. 2021;13:a039867
  111. 111. Akhtar SS, Mekureyaw MF, Pandey C, Roitsch T. Role of cytokinins for interactions of plants with microbial pathogens and pest insects. Frontiers in Plant Science. 2020;10:1777
  112. 112. Wu W, Du K, Kang X, Wei H. The diverse roles of cytokinins in regulating leaf development. Horticulture Research. 2021;8:1-13
  113. 113. McGuiness PN, Reid JB, Foo E. The role of gibberellins and brassinosteroids in nodulation and arbuscular mycorrhizal associations. Frontiers in Plant Science. 2019;10
  114. 114. Park Y-G, Mun B-G, Kang S-M, Hussain A, Shahzad R, Seo C-W, et al. Bacillus aryabhattai SRB02 tolerates oxidative and nitrosative stress and promotes the growth of soybean by modulating the production of phytohormones. PLoS ONE. 2017;12:e0173203
  115. 115. Ryu C-M, Farag MA, Hu C-H, Reddy MS, Wei H-X, Paré PW, et al. Bacterial volatiles promote growth in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 2003;100:4927-4932
  116. 116. Yi H-S, Ahn Y-R, Song GC, Ghim S-Y, Lee S, Lee G, et al. Impact of a bacterial volatile 2,3-butanediol on Bacillus subtilis rhizosphere robustness. Frontiers in Microbiology. 2016;7:993
  117. 117. Shemshura ON, Shemsheyeva ZN, Sadanov AK, Alimzhanova MB, Daugaliyeva ST, Mombekova GA, et al. Plant growth promotion by volatile organic compounds produced by Chryseobacterium rhizoplanae isolated from Vigna radiata. Ecology. Environment & Conservation. 2019;25:807-812
  118. 118. Sharifi R, Ryu C-M. Revisiting bacterial volatile-mediated plant growth promotion: lessons from the past and objectives for the future. Annals of Botany. 2018;122:349-358
  119. 119. Bai Y, D’Aoust F, Smith DL, Driscoll BT. Isolation of plant-growth-promoting Bacillus strains from soybean root nodules. Canadian Journal of Microbiology. 2002;48:230-238
  120. 120. Carreño-López R, Alatorre-Cruz JM, Marín-Cevada V. Pyrroloquinoline quinone (PQQ): Role in plant-microbe interactions. In: Singh HB, Keswani C, Reddy MS, Sansinenea E, García-Estrada C, editors. Secondary Metabolites of Plant Growth Promoting Rhizomicroorganisms: Discovery and Applications. Singapore: Springer; 2019. pp. 169-184
  121. 121. Mishra S, Kumar S, Saha B, Awasthi J, Dey M, Panda SK, et al. Crosstalk between salt, drought, and cold stress in plants: Toward genetic engineering for stress tolerance. In: Abiotic Stress Response in Plants. Weinheim, Germany: John Wiley & Sons, Ltd; 2016. page 57-88.
  122. 122. Sturz AV, Christie BR. Endophytic bacteria of red clover as agents of allelopathic clover-maize syndromes. Soil Biology and Biochemistry. 1996;28:583-588
  123. 123. Mallik MAB, Tesfai K. Allelopathic effect of common weeds on soybean growth and soybean-Bradyrhizobium symbiosis. Plant and Soil. 1988;112:177-182
  124. 124. Bulgarelli D, Rott M, Schlaeppi K, Loren V, van Themaat E, Ahmadinejad N, et al. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature. 2012;488:91-95
  125. 125. Compant S, Clément C, Sessitsch A. Plant growth-promoting bacteria in the rhizoand endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization. Soil Biology and Biochemistry. 2010;42:669-678
  126. 126. Miller MB, Bassler BL. Quorum sensing in bacteria. Annual Review of Microbiology. 2001;55:165-199
  127. 127. Pieterse CMJ, Zamioudis C, Berendsen RL, Weller DM, Wees SCMV, Bakker PAHM. Induced systemic resistance by beneficial microbes. Annual Review of Phytopathology. 2014;52:347-375
  128. 128. Gunatilaka AAL. Natural products from plant-associated microorganisms: Distribution, structural diversity, bioactivity, and implications of their occurrence. Journal of Natural Products. 2006;69:509-526
  129. 129. Martinez-Klimova E, Rodríguez-Peña K, Sánchez S. Endophytes as sources of antibiotics. Biochemical Pharmacology. 2017;134:1-17
  130. 130. Morales-Cedeño LR, Orozco-Mosqueda M d C, Loeza-Lara PD, Parra-Cota FI, de los Santos-Villalobos S, Santoyo G. Plant growth-promoting bacterial endophytes as biocontrol agents of pre- and post-harvest diseases: Fundamentals, methods of application and future perspectives. Microbiological Research. 2021;242:126612
  131. 131. Coutte F, Lecouturier D, Dimitrov K, Guez J-S, Delvigne F, Dhulster P, et al. Microbial lipopeptide production and purification bioprocesses, current progress and future challenges. Biotechnology Journal. 2017;12:1600566
  132. 132. Tripathi S, Kamal S, Sheramati I, Oelmuller R, Varma A. Mycorrhizal fungi and other root endophytes as biocontrol agents against root pathogens. In: Varma A, editor. Mycorrhiza: State of the Art, Genetics and Molecular Biology, Eco-Function, Biotechnology, Eco-Physiology, Structure and Systematics. Berlin, Heidelberg: Springer; 2008. pp. 281-306
  133. 133. Gao F-K, Dai C-C, Liu X-Z. Mechanisms of fungal endophytes in plant protection against pathogens. African Journal of Microbiology Research. 2010;4:1346-1351
  134. 134. Blumer C, Haas D. Mechanism, regulation, and ecological role of bacterial cyanide biosynthesis. Archives of Microbiology. 2000;173:170-177
  135. 135. Zaghloul RA, Abou-Aly HE, Tewfike TA, Ashry NM. Isolation and characterization of endophytic bacteria isolated from legumes and non-legumes plants in Egypt. Journal of Pure and Applied Microbiology. 2016;10:277-290
  136. 136. Beneduzi A, Ambrosini A, Passaglia LMP. Plant growth-promoting rhizobacteria (PGPR): Their potential as antagonists and biocontrol agents. Genetics and Molecular Biology. 2012;35:1044-1051
  137. 137. Tariq M, Noman M, Ahmed T, Hameed A, Manzoor N, Zafar M. Antagonistic features displayed by plant growth promoting rhizobacteria (PGPR): A review. Journal of Plant Science and Phytopathology. 2017;1:38-43
  138. 138. Bahroun A, Jousset A, Mhamdi R, Mrabet M, Mhadhbi H. Anti-fungal activity of bacterial endophytes associated with legumes against Fusarium solani: Assessment of fungi soil suppressiveness and plant protection induction. Applied Soil Ecology. 2018;124:131-140
  139. 139. Brameyer S, Bode HB, Heermann R. Languages and dialects: Bacterial communication beyond homoserine lactones. Trends in Microbiology. 2015;23:521-523
  140. 140. Von Bodman SB, Bauer WD, Coplin DL. Quorum sensing in plant-pathogenic bacteria. Annual Review of Phytopathology. 2003;41:455-482
  141. 141. Dong YH, Wang LH, Xu JL, Zhang HB, Zhang XF, Zhang LH. Quenching quorumsensing-dependent bacterial infection by an N-acyl homoserine lactonase. Nature. 2001;411:813-817
  142. 142. Achari GA, Ramesh R. Recent advances in quorum quenching of plant pathogenic bacteria. In: Meena SN, Naik MM, editors. Advances in Biological Science Research. NY, USA: Academic Press; 2019. pp. 233-245
  143. 143. Lopes RBM, Costa LE d O, MCD V, de Araújo EF, de Queiroz MV. Endophytic bacteria isolated from common bean (Phaseolus vulgaris) exhibiting high variability showed antimicrobial activity and quorum sensing inhibition. Current Microbiology. 2015;71:509-516
  144. 144. Maksimov I, Maksimova T, Sarvarova E, Blagova D, Popov V. Endophytic bacteria as effective agents of new-generation biopesticides (review). Applied Biochemistry and Microbiology. 2018;54:128-140
  145. 145. Flury P, Vesga P, Péchy-Tarr M, Aellen N, Dennert F, Hofer N, et al. Antimicrobial and insecticidal: Cyclic lipopeptides and hydrogen cyanide produced by plant-beneficial Pseudomonas Strains CHA0, CMR12a, and PCL1391 contribute to insect killing. Frontiers in Microbiology. 2017;8:100
  146. 146. Berry C. The bacterium, Lysinibacillus sphaericus, as an insect pathogen. Journal of Invertebrate Pathology. 2012;109:1-10
  147. 147. Pérez-Montaño F, Alías-Villegas C, Bellogín RA, del Cerro P, Espuny MR, Jiménez-Guerrero I, et al. Plant growth promotion in cereal and leguminous agricultural important plants: From microorganism capacities to crop production. Microbiological Research. 2014;169:325-336
  148. 148. Abdul Malik NA, Kumar IS, Nadarajah K. Elicitor and receptor molecules: Orchestrators of plant defense and immunity. International Journal of Molecular Sciences. 2020;21:963
  149. 149. Bakker P, Berendsen R, Doornbos R, Wintermans P, Pieterse C. The rhizosphere revisited: Root microbiomics. Frontiers in Plant Science. 2013;4:165
  150. 150. Araújo SS, Beebe S, Crespi M, Delbreil B, González EM, Gruber V, et al. Abiotic stress responses in legumes: Strategies used to cope with environmental challenges. Critical Reviews in Plant Sciences. 2015;34:237-280
  151. 151. Guzzo MC, Costamagna C, Salloum MS, Rotundo JL, Monteoliva MI, Luna CM. Morpho-physiological traits associated with drought responses in soybean. Crop Science. 2021;61:672-688
  152. 152. Monteoliva MI, Guzzo MC, Posada GA. Breeding for drought tolerance by monitoring chlorophyll content. Gene Technology. 2021;10:1-10
  153. 153. Devireddy AR, Zandalinas SI, Fichman Y, Mittler R. Integration of reactive oxygen species and hormone signaling during abiotic stress. The Plant Journal. 2021;105:459-476
  154. 154. Cejudo FJ, Sandalio LM, Van Breusegem F. Understanding plant responses to stress conditions: redox-based strategies. Journal of Experimental Botany. 2021;72:5785-5788
  155. 155. Shukla PS, Agarwal PK, Jha B. Improved salinity tolerance of Arachishypogaea (L.) by the interaction of halotolerant plant-growth-promoting rhizobacteria. Journal of Plant Growth Regulation. 2012;31:195-206
  156. 156. Khan MA, Asaf S, Khan AL, Ullah I, Ali S, Kang S-M, et al. Alleviation of salt stress response in soybean plants with the endophytic bacterial isolate Curtobacterium sp. SAK1. Annales de Microbiologie. 2019;69:797-808
  157. 157. Vaishnav A, Kumari S, Jain S, Varma A, Tuteja N, Choudhary DK. PGPR-mediated expression of salt tolerance gene in soybean through volatiles under sodium nitroprusside. Journal of Basic Microbiology. 2016;56:1274-1288
  158. 158. Dubey A, Saiyam D, Kumar A, Hashem A, Abd_Allah EF, Khan ML. Bacterial root endophytes: Characterization of their competence and plant growth promotion in soybean (Glycine max(L.) Merr.) under drought stress. International Journal of Environmental Research and Public Health. 2021;18:931
  159. 159. Ullah A, Nisar M, Ali H, Hazrat A, Hayat K, Keerio AA, et al. Drought tolerance improvement in plants: An endophytic bacterial approach. Applied Microbiology and Biotechnology. 2019;103:7385-7397
  160. 160. Asaf S, Khan AL, Khan MA, Imran QM, Yun B-W, Lee I-J. Osmoprotective functions conferred to soybean plants via inoculation with Sphingomonas sp. LK11 and exogenous trehalose. Microbiological Research. 2017;205:135-145
  161. 161. Suárez R, Wong A, Ramírez M, Barraza A, Orozco MDC, Cevallos MA, et al. Improvement of drought tolerance and grain yield in common bean by overexpressing trehalose-6-phosphate synthase in rhizobia. Molecular Plant-Microbe Interactions. 2008;21:958-966
  162. 162. Sharma MP, Grover M, Chourasiya D, Bharti A, Agnihotri R, Maheshwari HS, et al. Deciphering the role of trehalose in tripartite symbiosis among rhizobia, arbuscular mycorrhizal fungi, and legumes for enhancing abiotic stress tolerance in crop plants. Frontiers in Microbiology. 2020;11:509919
  163. 163. Pieterse CMJ, Van der Does D, Zamioudis C, Leon-Reyes A, Van Wees SCM. Hormonal modulation of plant immunity. Annual Review of Cell and Developmental Biology. 2012;28:489-521
  164. 164. Abeles FB, Morgan PV, Saltveit ME, editors. Ethylene in Plant Biology. 2nd ed. New York, US: Academic Press; 1992
  165. 165. Ravanbakhsh M, Sasidharan R, Voesenek LACJ, Kowalchuk GA, Jousset A. Microbial modulation of plant ethylene signaling: Ecological and evolutionary consequences. Microbiome. 2018;6:52
  166. 166. Glick BR. Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiological Research. 2014;169:30-39
  167. 167. Gupta S, Pandey S. ACC deaminase producing bacteria with multifarious plant growth promoting traits alleviates salinity stress in French Bean (Phaseolus vulgaris) plants. Frontiers in Microbiology. 2019;10:1506
  168. 168. Chinnaswamy A, de la Peña TC, Stoll A, Rojo D d l P, Bravo J, Rincón A, et al. A nodule endophytic Bacillus megaterium strain isolated from Medicago polymorpha enhances growth, promotes nodulation by Ensifer medicae and alleviates salt stress in alfalfa plants. Annals of Applied Biology. 2018;172:295-308
  169. 169. de Zélicourt A, Synek L, Saad MM, Alzubaidy H, Jalal R, Xie Y, et al. Ethylene induced plant stress tolerance by Enterobacter sp. SA187 is mediated by 2-keto-4-methylthiobutyric acid production. PLoS Genetics. 2018;14:e1007273
  170. 170. Patten CL, Glick BR. Bacterial biosynthesis of indole-3-acetic acid. Canadian Journal of Microbiology. 1996;42:207-220
  171. 171. Khalid A, Tahir S, Arshad M, Zahir ZA, Khalid A, Tahir S, et al. Relative efficiency of rhizobacteria for auxin biosynthesis in rhizosphere and non-rhizosphere soils. Soil Research. 2004;42:921-926
  172. 172. Swarnalakshmi K, Yadav V, Tyagi D, Dhar DW, Kannepalli A, Kumar S. Significance of plant growth promoting rhizobacteria in grain legumes: Growth promotion and crop production. Plants (Basel). 2020;9:1596
  173. 173. Zaheer A, Mirza BS, Mclean JE, Yasmin S, Shah TM, Malik KA, et al. Association of plant growth-promoting Serratia spp. with the root nodules of chickpea. Research in Microbiology. 2016;167:510-520
  174. 174. Egamberdieva D, Wirth SJ, Shurigin VV, Hashem A, Abd-Allah EF. Endophytic bacteria improve plant growth, symbiotic performance of chickpea (Cicer arietinumL.) and induce suppression of root rot caused byFusarium solaniunder salt stress. Frontiers in Microbiology. 1887;2017:8
  175. 175. Paul D, Lade H. Plant-growth-promoting rhizobacteria to improve crop growth in saline soils: A review. Agronomy for Sustainable Development. 2014;34:737-752
  176. 176. de Souza RSC, Armanhi JSL, Arruda P. From microbiome to traits: Designing synthetic microbial communities for improved crop resiliency. Frontiers in Plant Science. 2020;11:1179
  177. 177. Großkopf T, Soyer OS. Synthetic microbial communities. Current Opinion in Microbiology. 2014;18:72-77
  178. 178. Quiza L, St-Arnaud M, Yergeau E. Harnessing phytomicrobiome signaling for rhizosphere microbiome engineering. Frontiers in Plant Science. 2015;6:507
  179. 179. Kumar A, Dubey A. Rhizosphere microbiome: Engineering bacterial competitiveness for enhancing crop production. Journal of Advanced Research. 2020;24:337-352
  180. 180. Korir H, Mungai NW, Thuita M, Hamba Y, Masso C. Co-inoculation effect of rhizobia and plant growth promoting rhizobacteria on common bean growth in a low phosphorus soil. Frontiers in Plant Science. 2017;8:141
  181. 181. Becker J, Eisenhauer N, Scheu S, Jousset A. Increasing antagonistic interactions cause bacterial communities to collapse at high diversity. Ecology Letters. 2012;15:468-474
  182. 182. Ray P, Lakshmanan V, Labbé JL, Craven KD. Microbe to microbiome: A paradigm shift in the application of microorganisms for sustainable agriculture. Frontiers in Microbiology. 2020;11:622926
  183. 183. Pérez-Jaramillo JE, de Hollander M, Ramírez CA, Mendes R, Raaijmakers JM, Carrión VJ. Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia. Microbiome. 2019;7:114
  184. 184. Mendes LW, de Chaves MG, Fonseca M d C, Mendes R, Raaijmakers JM, Tsai SM, et al. Frontiers in Microbiology. 2019;10:2252
  185. 185. Venter ZS, Jacobs K, Hawkins H-J. The impact of crop rotation on soil microbial diversity: A meta-analysis. Pedobiologia. 2016;59:215-223
  186. 186. Pivato B, Semblat A, Guégan T, Jacquiod S, Martin J, Deau F, et al. Rhizosphere bacterial networks, but not diversity, are impacted by pea-wheat intercropping. Frontiers in Microbiology. 2021;12:674556
  187. 187. Ellouze W, Hamel C, Vujanovic V, Gan Y, Bouzid S, St-Arnaud M. Chickpea genotypes shape the soil microbiome and affect the establishment of the subsequent durum wheat crop in the semiarid North American Great Plains. Soil Biology and Biochemistry. 2013;63:129-141
  188. 188. Sturz AV, Christie BR, Matheson BG. Associations of bacterial endophyte populations from red clover and potato crops with potential for beneficial allelopathy. Canadian Journal of Microbiology. 1998;44:162-167
  189. 189. Zhang J, Cook J, Nearing JT, Zhang J, Raudonis R, Glick BR, et al. Harnessing the plant microbiome to promote the growth of agricultural crops. Microbiological Research. 2021;245:126690

Written By

Mariela I. Monteoliva, Lucio Valetti, Tania Taurian, Clara S. Crociara and María Carla Guzzo

Submitted: September 19th, 2021 Reviewed: January 7th, 2022 Published: March 31st, 2022