Biofilm formation is determinant in tomato rhizosphere colonization by Bacillus velezensis FZB42

Mitigating sediment cadmium contamination through combining PGPR Enterobacter ludwigii with the submerged macrophyte Vallisneria natans

Sediment cadmium contamination poses risks to aquatic ecosystems. Phytoremediation is an environmentally sustainable method to mitigate cadmium contamination. Submerged macrophytes are affected by cadmium stress, but plant growth-promoting rhizobacteria (PGPR) can restore the health status of submerged macrophytes. Herein, we aimed to reduce sediment cadmium concentration and reveal the mechanism by which the combined application of the PGPR Enterobacter ludwigii and the submerged macrophyte Vallisneria natans mitigates cadmium contamination. Sediment cadmium concentration decreased by 21.59% after submerged macrophytes were planted with PGPR, probably because the PGPR colonized the rhizosphere and roots of the macrophytes. The PGPR induced a 5.09-fold increase in submerged macrophyte biomass and enhanced plant antioxidant response to cadmium stress, as demonstrated by decreases in oxidative product levels (reactive oxygen species and malondialdehyde), which corresponded to shift in rhizosphere metabolism, notably in antioxidant defence systems (i.e., the peroxidation of linoleic acid into 9-hydroperoxy-10E,12Z-octadecadienoic acid) and in some amino acid metabolism pathways (i.e., arginine and proline). Additionally, PGPR mineralized carbon in the sediment to promote submerged macrophyte growth. Overall, PGPR mitigated sediment cadmium accumulation via a synergistic plantmicrobe mechanism. This work revealed the mechanism by which PGPR and submerged macrophytes control cadmium concentration in contaminated sediment.

Insights into the biocontrol and plant growth promotion functions of Bacillus altitudinis strain KRS010 against Verticillium dahliae

BACKGROUND

Verticillium wilt, caused by the fungus Verticillium dahliae, is a soil-borne vascular fungal disease, which has caused great losses to cotton yield and quality worldwide. The strain KRS010 was isolated from the seed of Verticillium wilt-resistant Gossypium hirsutum cultivar "Zhongzhimian No. 2."

RESULTS

The strain KRS010 has a broad-spectrum antifungal activity to various pathogenic fungi as Verticillium dahliae, Botrytis cinerea, Fusarium spp., Colletotrichum spp., and Magnaporthe oryzae, of which the inhibition rate of V. dahliae mycelial growth was 73.97% and 84.39% respectively through confrontation test and volatile organic compounds (VOCs) treatments. The strain was identified as Bacillus altitudinis by phylogenetic analysis based on complete genome sequences, and the strain physio-biochemical characteristics were detected, including growth-promoting ability and active enzymes. Moreover, the control efficiency of KRS010 against Verticillium wilt of cotton was 93.59%. After treatment with KRS010 culture, the biomass of V. dahliae was reduced. The biomass of V. dahliae in the control group (Vd991 alone) was 30.76-folds higher than that in the treatment group (KRS010+Vd991). From a molecular biological aspect, KRS010 could trigger plant immunity by inducing systemic resistance (ISR) activated by salicylic acid (SA) and jasmonic acid (JA) signaling pathways. Its extracellular metabolites and VOCs inhibited the melanin biosynthesis of V. dahliae. In addition, KRS010 had been characterized as the ability to promote plant growth.

CONCLUSIONS

This study indicated that B. altitudinis KRS010 is a beneficial microbe with a potential for controlling Verticillium wilt of cotton, as well as promoting plant growth.

ccdC Regulates Biofilm Dispersal in Bacillus velezensis FZB42

Bacillus velezensis FZB42 is a plant growth-promoting rhizobacterium (PGPR) and a model microorganism for biofilm studies. Biofilms are required for the colonization and promotion of plant growth in the rhizosphere. However, little is known about how the final stage of the biofilm life cycle is regulated, when cells regain their motility and escape the mature biofilm to spread and colonize new niches. In this study, the non-annotated gene ccdC was found to be involved in the process of biofilm dispersion. We found that the ccdC-deficient strain maintained a wrinkled state at the late stage of biofilm formation in the liquid-gas interface culture, and the bottom solution showed a clear state, indicating that no bacterial cells actively escaped, which was further evidenced by the formation of a cellular ring (biofilm pellicle) located on top of the preformed biofilm. It can be concluded that dispersal, a biofilm property that relies on motility proficiency, is also positively affected by the unannotated gene ccdC. Furthermore, we found that the level of cyclic diguanylate (c-di-GMP) in the ccdC-deficient strain was significantly greater than that in the wild-type strain, suggesting that B. velezensis exhibits a similar mechanism by regulating the level of c-di-GMP, the master regulator of biofilm formation, dispersal, and cell motility, which controls the fitness of biofilms in Pseudomonas aeruginosain. In this study, we investigated the mechanism regulating biofilm dispersion in PGPR.

Enhancing tomato disease resistance through endogenous antifungal proteins and introduced nematode-targeting dsRNA of biocontrol agent Bacillus velezensis HS-3

BACKGROUND

As a type of biological control agent (BCA), Bacillus velezensis possesses the efficacy of inhibiting pathogenic microorganisms, promoting plant growth, and overcoming continuous cropping obstacles (CCOs). However, there is limited reporting on the optimization of the cultivation conditions for such biocontrol agents and their role as double-stranded RNA (dsRNA) delivery vectors.

RESULTS

In this study, a Bacillus velezensis strain HS-3 was isolated from the root zone of tomato plants with in vitro anti-Botrytis cinerea activity. The investigation into active compounds revealed that HS-3 predominantly employs proteins with molecular weights greater than 3 kDa for its antifungal activity. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis identified various proteases and chitosanase, further suggesting that HS-3 most likely employs these enzymes to degrade fungal cell walls for its antifungal effect. To optimize the production of extracellular proteins, fermentation parameters for HS-3 were systematically optimized, leading to an optimized medium (OP-M). HS-3 cultured in OP-M demonstrated enhanced capacity to assist tomato plants in withstanding CCOs. However, the presence of excessive nematodes in diseased soil resulted in the disease severity index (DSI) remaining high. An RNA interference mechanism was further introduced to HS-3, targeting the nematode tyrosine phosphatase (TP) gene. Ultimately, HS-3 expressing dsRNA of TP in OP-M effectively assisted tomatoes in mitigating CCOs, reducing DSI to 2.2% and 17.8% of the control after 45 and 90 days of growth, respectively.

CONCLUSION

The advantages of Bacillus velezensis in crop disease management and the mitigation of CCOs become even more pronounced when utilizing both optimized levels of endogenous enzymes and introduced nematode-targeting dsRNA. © 2024 Society of Chemical Industry.

Analysis of antimicrobial biological activity of a marine Bacillus velezensis NDB

A new strain of Bacillus velezensis NDB was isolated from Xiangshan Harbor and antibacterial test revealed antibacterial activity of this strain against 12 major pathogenic bacteria. The whole genome of the bacterium was sequenced and found to consist of a 4,214,838 bp circular chromosome and a 7410 bp circular plasmid. Furthermore, it was predicted by AntiSMASH and BAGEL4 to have 12 clusters of secondary metabolism genes for the synthesis of the inhibitors, fengycin, bacillomycin, macrolactin H, bacillaene, and difficidin, and there were also five clusters encoding potentially novel antimicrobial substances, as well as three bacteriocin biosynthesis gene clusters of amylocyclicin, ComX1, and LCI. qRT-PCR revealed significant up-regulation of antimicrobial secondary metabolite synthesis genes after 24 h of antagonism with pathogenic bacteria. Furthermore, MALDI-TOF mass spectrometry revealed that it can secrete surfactin non-ribosomal peptide synthase and polyketide synthase to exert antibacterial effects. GC-MS was used to analyze methanol extract of B. velezensis NDB, a total of 68 compounds were identified and these metabolites include 16 amino acids, 17 acids, 3 amines, 11 sugars, 11 alcohols, 1 ester, and 9 other compounds which can inhibit pathogenic bacteria by initiating the antibiotic secretion pathway. A comparative genomic analysis of gene families showed that the specificity of B. velezensis NDB was mainly reflected in environmental adaptability. Overall, this research on B. velezensis NDB provides the basis for elucidating its biocontrol effect and promotes its future application as a probiotic.

Phosphate-Solubilizing Bacillus sp. Modulate Soil Exoenzyme Activities and Improve Wheat Growth

Phosphorus (P) is a vital mineral nutrient in agriculture and its deficiency results in reduced growth, yield, and grain quality in cereals. Much of the applied P in agriculture becomes fixed in soils, limiting its accessibility to plants. Thus, investigating sustainable strategies to release fixed P resources and enhance plant uptake is crucial. This study explored how plant-associated bacteria employ phosphate solubilizing mechanisms to improve P availability. The growth patterns of four bacterial strains, namely Bacillus subtilis ZE15 and ZR3, along with Bacillus megaterium ZE32 and ZR19, were examined in Pikovskaya's broth culture with and without the addition of insoluble phosphorus (P). In the absence of P amendment, most strains reached a stationary growth phase by the fourth day. However, their responses diverged when exposed to P-amended media. Particularly, ZE15 demonstrated the highest P solubilization capability, achieving up to 130 µg mL-1 solubilization in vitro. All strains produced organic acids in Pikovskaya's broth culture. A comparison of the influence of Ca3(PO4)2 revealed significantly greater organic acid quantities in the presence of insoluble P. Notably, strain ZE15 exhibited the highest phosphate esterase activity (3.65 nmol g-1 dry matter), while strain ZE32 showed the highest ß-D glucosidase activity (2.81 nmol g-1 dry matter) in the presence of insoluble P. The ability of Bacillus species to solubilize P in combination with increased exoenzyme activity in the rhizosphere could be used in future studies to support P uptake through enhanced solubilization and mineralization.

Phosphate-solubilizing bacteria: Their agroecological function and optimistic application for enhancing agro-productivity

Phosphorus (P) is a limiting nutrient in the soil-plant nutrient cycling. Although the exogenous application of chemical P fertilizers can satisfy crop P requirements during critical growth phases. While excessive P fertilizers use results in low phosphorus acquisition efficiency (PAE), it has serious environmental consequences and hastens the depletion of P mineral reserves. Phosphate-solubilizing bacteria (PSB) have the potential to make insoluble phosphate available to plants through solubilization and mineralization, increasing crop yields while maintaining environmental sustainability. Existing reviews mainly focus on the beneficial effects of PSB on crop performance and related mechanisms, while few of them elucidate the action mechanisms of PSB in soil-microbe-plant interactions for crop cultivation with high yield efficiency. Hence, this study provides a comprehensive review of the physicochemical and molecular mechanisms (e.g., root exudates, extracellular polysaccharides, organic acids, phosphatases, and phosphate-specific transport systems) of PSB to facilitate the P cycle in the soil-plant systems. Further, the potential of commercial applications of PSB (e.g., genetic engineering, seed priming and coating) are also discussed in order to highlight their contribution to sustainable agriculture. Finally, existing challenges and future prospects in agricultural applications are proposed. In conclusion, we firmly believe that PSB represent a highly significant biotechnological tool for enhancing agricultural productivity and offers a wide range of extensive potential applications.

Pectic homogalacturonan sensed by Bacillus acts as host associated cue to promote establishment and persistence in the rhizosphere

Bacillus velezensis isolates are among the most promising plant-associated beneficial bacteria used as biocontrol agents. However, various aspects of the chemical communication between the plant and these beneficials, determining root colonization ability, remain poorly described. Here we investigated the molecular basis of such interkingdom interaction occurring upon contact between Bacillus velezensis and its host via the sensing of pectin backbone homogalacturonan (HG). We showed that B. velezensis stimulates key developmental traits via a dynamic process involving two conserved pectinolytic enzymes. This response integrates transcriptional changes leading to the switch from planktonic to sessile cells, a strong increase in biofilm formation, and an accelerated sporulation dynamics while conserving the potential to efficiently produce specialized secondary metabolites. As a whole, we anticipate that this response of Bacillus to cell wall-derived host cues contributes to its establishment and persistence in the competitive rhizosphere niche and ipso facto to its activity as biocontrol agent.

Calendula officinalis-A Great Source of Plant Growth Promoting Endophytic Bacteria (PGPEB) and Biological Control Agents (BCA)

The application of beneficial bacteria may present an alternative approach to chemical plant protection and fertilization products as they enhance growth and resistance to biotic and abiotic stresses. Plant growth-promoting bacteria are found in the rhizosphere, epiphytically or endophytically (Plant Growth Promoting Endophytic Bacteria, PGPEB). In the present study, 36 out of 119 isolated endophytic bacterial strains from roots, leaves and flowers of the pharmaceutical plant Calendula officinalis were further identified and classified into Bacillus, Pseudomonas, Pantoea, Stenotrophomonas and Rhizobium genera. Selected endophytes were evaluated depending on positive reaction to different plant growth promoting (PGP) traits, motility, survival rate and inhibition of phytopathogenic fungi in vitro and ex vivo (tomato fruit). Bacteria were further assessed for their plant growth effect on Arabidopsis thaliana seedlings and on seed bio-primed tomato plantlets, in vitro. Our results indicated that many bacterial endophytes increased seed germination, promoted plant growth and changed root structure by increasing lateral root density and length and root hair formation. The most promising antagonistic PGPEB strains (Cal.r.29, Cal.l.30, Cal.f.4, Cal.l.11, Cal.f.2.1, Cal.r.19 and Cal.r.11) are indicated as effective biological control agents (BCA) against Botrytis cinerea on detached tomato fruits. Results underlie the utility of beneficial endophytic bacteria for sustainable and efficient crop production and disease control.

Impact of soil types and root exudates on cadmium and petroleum hydrocarbon phytoremediation by Sorghum sudanense, Festuca arundinace, and Lolium perenne

With the development of industrialization, soils around the world have been polluted by heavy metals and oil to different degrees in recent years, and soil remediation has become a global problem. Phytoremediation has a wide application prospect because of its environmental friendliness and easy availability of materials.

Objective

To explore the effects of soil types and root exudates on the removal of cadmium and petroleum hydrocarbon in soils.

Method

A pot experiments with three soil types (sandy, loamy and clayey) of the Changning-Weiyuan area of Sichuan province and three root exudates (citric acid, glycine, and maltose) were carried out using Sorghum sudanense (Piper) Stapf., Lolium perenne L., and Festuca arundinacea L. as test materials. Plants were grown in soils contaminated by cadmium and petroleum at different concentrations.

Result

The biomass of S. sudanense, the translocation ratio and removal rate of cadmium in S. sudanense decreased gradually with increasing soil cadmium concentration. The promotion effects of the three root exudates on S. sudanense were in the following order: citric acid > glycine > maltose. At the same cadmium pollution conditions, the biomass levels of S. sudanense in sandy, loamy, and clayey soils were in the following order: clayey soil > loamy soil > sandy soil. On the contrary, the concentration, translocation ratio, and removal rate of cadmium in S. sudanense grown in the different soils treated with root exudates were in the following order: sandy soil > loamy soil > clayey soil. Under the three soil conditions, the fresh weight of F. arundinacea (0.36 ~ 0.68 g) and S. sudanense (0.51 ~ 0.99 g) increased significantly (p < 0.05). The total petroleum hydrocarbons degradation efficiencies of F. arundinacea, L. perenne, and S. sudanense were high in sandy soil (34.27% ~ 60.52%). Changing the type of root exudate had a significant impact on the degradation of total petroleum hydrocarbons in sandy soil (p < 0.05).

Conclusion

This study showed that soil types impacted the accumulation of cadmium and petroleum in plants. Phytoremediation of cadmium and petroleum contaminated soil could be enhanced by the application of root exudates. This study recommend that the method is suitable for field remediation of soils contaminated with mild cadmium and petroleum hydrocarbons.

Characterization of Bacillus velezensis RDA1 as a Biological Control Agent against White Root Rot Disease Caused by Rosellinia necatrix

White root rot disease, caused by Rosellinia necatrix, poses a threat to several tree crops; hence, effective and sustainable strategies to control this disease remain warranted. This study identified an effective R. necatrix biocontrol agent by isolating 32 strains from soil samples collected from white root rot-infested organic pear orchards, among which RDA1 exhibited the most potent growth-inhibitory effects. Microbiological and 16S rRNA gene sequencing analyses revealed that the bacterial isolate belonged to the Bacillus genus and exhibited 100% nucleotide sequence similarity with Bacillus velezensis species in the GenBank. This strain showed strong antifungal activity against four Rosellinia necatrix strains and harbored genes essential for lipopeptide, polyketide, and tripeptide bacilysin biosynthesis. RDA1 produced volatile compounds that suppressed the development of phytopathogens and possessed plant growth-promoting traits, such as phosphate solubilization, and indole-3-acetic acid and siderophore production. B. velezensis RDA1 has a significant potential application in sustainable agriculture and can be used to suppress white root rot disease infections and to improve plant growth.

Comparative Genomics Insights into a Novel Biocontrol Agent Paenibacillus peoriae Strain ZF390 against Bacterial Soft Rot

Simple Summary

Bacterial soft rot, attributed to Pectobacterium brasiliense infection, has caused destructive impacts and colossal economic losses to China’s agricultural industry. Chemical control, which was ubiquitously used, cannot manage this disease as expected, so biocontrol has been followed with interest to date. In this study, we found a Paenibacillus peoriae strain ZF390 that had a potent control efficiency over cucumber plants against Pectobacterium brasiliense, and the comparative genomic analysis revealed biocontrol mechanisms might be involved in the strain ZF390.

Abstract

Bacterial soft rot, caused by Pectobacterium brasiliense, can infect several economically important horticultural crops. However, the management strategies available to control this disease are limited. Plant-growth-promoting rhizobacteria (PGPR) have been considered to be promising biocontrol agents. With the aim of obtaining a strain suitable for agricultural applications, 161 strains were isolated from the rhizosphere soil of healthy cucumber plants and screened through plate bioassays and greenhouse tests. Paenibacillus peoriae ZF390 exhibited an eminent control effect against soft rot disease and a broad antagonistic activity spectrum in vitro. Moreover, ZF390 showed good activities of cellulase, protease, and phosphatase and a tolerance of heavy metal. Whole-genome sequencing was performed and annotated to explore the underlying biocontrol mechanisms. Strain ZF390 consists of one 6,193,667 bp circular chromosome and three plasmids. Comparative genome analysis revealed that ZF390 involves ten gene clusters responsible for secondary metabolite antibiotic synthesis, matching its excellent biocontrol activity. Plenty of genes related to plant growth promotion, biofilm formation, and induced systemic resistance were mined to reveal the biocontrol mechanisms that might consist in strain ZF390. Overall, these findings suggest that strain ZF390 could be a potential biocontrol agent in bacterial-soft-rot management, as well as a source of antimicrobial mechanisms for further exploitation.

New Insights into Bacillus-Primed Plant Responses to a Necrotrophic Pathogen Derived from the Tomato-Botrytis Pathosystem

Induced systemic resistance (ISR) is one of the most studied mechanisms of plant−microbe interaction and is considered a very promising alternative for integrated pest management programs. In our study, we explored the plant defense response induced by Bacillus velezensis BBC047 in relation to its application before or after Botrytis cinerea infection of tomato plants. The inoculation of BBC047 did not considerably alter the gene expression of the tomato tissues, whereas infection with B. cinerea in BBC047-primed plants induced expression of LRR and NBS-LRR receptors, which are highly related to the ISR response. As expected, B. cinerea infection generated molecular patterns typical of a defense response to pathogen infection as the overexpression of pathogenesis-related proteins (PRs) in leaflets distant to the point of infection. The curative treatment (P + F + B) allowed us to gain insights into plant response to an inverted priming. In this treatment, B. cinerea caused the m tissue damage, extending nearly entirely across the entire infected leaves. Additionally, genes generally associated with early SAR response (<16 h) were overexpressed, and apparently, the beneficial strain was not perceived as such. Therefore, we infer that the plant defense to the curative treatment represents a higher degree of biological stress triggered by the incorporation of strain BBC047 as second arriving microorganism. We highlight the importance the phytosanitary status of plants prior to inoculation of beneficial microorganism for the biocontrol of pathogens.

Rhizobiome engineering: Unveiling complex rhizosphere interactions to enhance plant growth and health

Crop plants are affected by a series of inhibitory environmental and biotic factors that decrease their growth and production. To counteract these adverse effects, plants work together with the microorganisms that inhabit their rhizosphere, which is part of the soil influenced by root exudates. The rhizosphere is a microecosystem where a series of complex interactions takes place between the resident microorganisms (rhizobiome) and plant roots. Therefore, this study analyzes the dynamics of plant-rhizobiome communication, the role of exudates (diffusible and volatile) as a factor in stimulating a diverse rhizobiome, and the differences between rhizobiomes of domesticated crops and wild plants. The study also analyzes different strategies to decipher the rhizobiome through both classical cultivation techniques and the so-called "omics" sciences. In addition, the rhizosphere engineering concept and the two general strategies to manipulate the rhizobiome, i.e., top down and bottom up engineering have been revisited. In addition, recent studies on the effects on the indigenous rhizobiome of inoculating plants with foreign strains, the impact on the endobiome, and the collateral effects on plant crops are discussed. Finally, understanding of the complex rhizosphere interactions and the biological repercussions of rhizobiome engineering as essential steps for improving plant growth and health is proposed, including under adverse conditions.

Molecular characterization of endophytic and ectophytic plant growth promoting bacteria isolated from tomato plants (Solanum lycopersicum L.) grown in different soil types

Background

Successful rhizosphere colonization by plant growth promoting rhizobacteria (PGPR) is of crucial importance to perform the desired plant growth promoting activities. Since rhizocompetence is a dynamic process influenced by surrounding environmental conditions. In the present study, we hypothesized that bacterial isolates obtained from different tomato plant microhabitats (balk soil, rhizosphere, endorhiza, phyllosphere, and endoshoot) grown in different soils (sand, clay, and peat moss) will show different rhizocompetence abilities.

Results

To evaluate this hypothesis, bacterial isolates were obtained from different plant microhabitats and screened for their phosphate solubilizing and nitrogen fixing activates. BOX-PCR fingerprint profiles showed high genotypic diversity among the tested isolates and that same genotypes were shared between different soils and/or plant microhabitats. 16S rRNA gene sequences of 25 PGP isolates, representing different plant spheres and soil types, were affiliated to eight genera: Enterobacter, Paraburkholderia, Klebsiella, Bacillus, Paenibacillus, Stenotrophomonas, Pseudomonas, and Kosakonia. The rhizocompetence of each isolate was evaluated in the rhizosphere of tomato plants grown on a mixture of the three soils. Different genotypes of the same bacterial species displayed different rhizocompetence potentials. However, isolates obtained from the above-ground parts of the plant showed high rhizocompetence. In addition, biological control-related genes, ituD and srfC, were detected in the obtained spore forming bacterial isolates.

Conclusion

This study evaluates, for the first time, the relationship between plant microhabitat and the rhizocompetence ability in tomato rhizosphere. The results indicated that soil type and plant sphere can influence both the genotypic diversity and rhizocompetence ability of the same bacterial species. Bacterial isolates obtained in this study are promising to be used as an environmentally friendly substitution of chemical fertilizers.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-022-00361-0.

Exopolysaccharides from Pantoea alhagi NX-11 specifically improve its root colonization and rice salt resistance

Plant growth-promoting rhizobacteria (PGPR) and their extracellular polymers such as exopolysaccharides can enhance rice salt stress resistance, however, the relevant mechanism remains unclear. In this study, an exopolysaccharides-deficient strain, named ΔpspD, was obtained from Pantoea alhagi NX-11 by chromosomal pspD deletion. The yield and characteristics of ΔpspD exopolysaccharides was obviously different from P. alhagi NX-11 exopolysaccharides (PAPS). Subsequently, hydroponic experiments showed that NX-11 or PAPS could enhance rice salt tolerance, but ΔpspD could not. Furthermore, it was found that PAPS promoted P. alhagi rhizosphere colonization through a direct effect on biofilm formation, as well as through an indirect impact of enhancing the abilities of biofilm formation and chemotaxis by altering rice root exudates. Importantly, the effect of PAPS in promoting the root colonization of NX-11 was specific. Through transcriptome and RT-qPCR analysis, we revealed that this specificity correlated with PAPS-induced lectin overexpression. The specificity between exopolysaccharides and the host microorganism ensures the colonization of the latter, and prevents other microorganisms from hitchhiking to the rice roots.

LC_Glucose-Inhibited Division Protein Is Required for Motility, Biofilm Formation, and Stress Response in Lysobacter capsici X2-3

Glucose-inhibited division protein (GidA) plays a critical role in the growth, stress response, and virulence of bacteria. However, how gidA may affect plant growth-promoting bacteria (PGPB) is still not clear. Our study aimed to describe the regulatory function of the gidA gene in Lysobacter capsici, which produces a variety of lytic enzymes and novel antibiotics. Here, we generated an LC_GidA mutant, MT16, and an LC_GidA complemented strain, Com-16, by plasmid integration. The deletion of LC_GidA resulted in an attenuation of the bacterial growth rate, motility, and biofilm formation of L. capsici. Root colonization assays demonstrated that the LC_GidA mutant showed reduced colonization of wheat roots. In addition, disruption of LC_GidA showed a clear diminution of survival in the presence of high temperature, high salt, and different pH conditions. The downregulated expression of genes related to DNA replication, cell division, motility, and biofilm formation was further validated by real-time quantitative PCR (RT–qPCR). Together, understanding the regulatory function of GidA is helpful for improving the biocontrol of crop diseases and has strong potential for biological applications.

Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions

Trophic interactions play a central role in driving microbial community assembly and function. In gut or soil ecosystems, successful inoculants are always facilitated by efficient colonization; however, the metabolite exchanges between inoculants and resident bacteria are rarely studied, particularly in the rhizosphere. Here, we used bioinformatic, genetic, transcriptomic, and metabonomic analyses to uncover syntrophic cooperation between inoculant (Bacillus velezensis SQR9) and plant-beneficial indigenous Pseudomonas stutzeri in the cucumber rhizosphere. We found that the synergistic interaction of these two species is highly environmental dependent, the emergence of syntrophic cooperation was only evident in a static nutrient-rich niche, such as pellicle biofilm in addition to the rhizosphere. Our results identified branched-chain amino acids (BCAAs) biosynthesis pathways are involved in syntrophic cooperation. Genome-scale metabolic modeling and metabolic profiling also demonstrated metabolic facilitation among the bacterial strains. In addition, biofilm matrix components from Bacillus were essential for the interaction. Importantly, the two-species consortium promoted plant growth and helped plants alleviate salt stress. In summary, we propose a mechanism in which synergic interactions between a biocontrol bacterium and a partner species promote plant health.

Relationship between lipopeptide biosurfactant and primary metabolite production by Bacillus strains in solid-state and submerged fermentation

The relationship between lipopeptide and primary metabolite production by Bacillus spp. in solid-state fermentation (SSF) and submerged fermentation (SmF) was evaluated. Four wild-type strains and one mutant strain (unable to develop biofilm) were assessed in SSF and SmF, using a defined medium and polyurethane foam as inert support for SSF. Strain ATCC 21,332 in SSF presented the highest lipopeptide production. The wild-type strains revealed higher lipopeptide and biomass production and lower synthesis of primary metabolites in SSF than in SmF. However, the mutant strain showed a slightly higher production of primary metabolites in SSF than in SmF. Carbon balance analysis showed that the carbon flux was mainly directed to lipopeptides in SSF, whereas in SmF, it was directed to the production of primary metabolites and the carbon flux to lipopeptides is inversely related to primary metabolites in both types of cultures.

Multiple Metabolic Phenotypes as Screening Criteria Are Correlated With the Plant Growth-Promoting Ability of Rhizobacterial Isolates

Efficient screening method is the prerequisite for getting plant growth-promoting (PGP) rhizobacteria (PGPR) which may play an important role in sustainable agriculture from the natural environment. Many current traditional preliminary screening criteria based on knowledge of PGP mechanisms do not always work well due to complex plant-microbe interactions and may lead to the low screening efficiency. More new screening criteria should be evaluated to establish a more effective screening system. However, the studies focused on this issue were not enough, and few new screening criteria had been proposed. The aim of this study was to analyze the correlation between the metabolic phenotypes of rhizobacterial isolates and their PGP ability. The feasibility of using these phenotypes as preliminary screening criteria for PGPR was also evaluated. Twenty-one rhizobacterial isolates were screened for their PGP ability, traditional PGP traits, and multiple metabolic phenotypes that are not directly related to PGP mechanisms, but are possibly related to rhizosphere colonization. Correlations between the PGP traits or metabolic phenotypes and increases in plant agronomic parameters were analyzed to find the indicators that are most closely related to PGP ability. The utilization of 11 nutrient substrates commonly found in root exudates, such as D-salicin, β-methyl-D-glucoside, and D-cellobiose, was significantly positively correlated with the PGP ability of the rhizobacterial isolates. The utilization of one amino acid and two organic acids, namely L-aspartic acid, α-keto-glutaric acid, and formic acid, was negatively correlated with PGP ability. There were no significant correlations between four PGP traits tested in this study and the PGP ability. The ability of rhizobacterial isolates to metabolize nutrient substrates that are identical or similar to root exudate components may act as better criteria than PGP traits for the primary screening of PGPR, because rhizosphere colonization is a prerequisite for PGPR to affect plants.

Genomic, Antimicrobial, and Aphicidal Traits of Bacillus velezensis ATR2, and Its Biocontrol Potential against Ginger Rhizome Rot Disease Caused by Bacillus pumilus

Ginger rhizome rot disease, caused by the pathogen Bacilluspumilus GR8, could result in severe rot of ginger rhizomes and heavily threaten ginger production. In this study, we identified and characterized a new Bacillus velezensis strain, designated ATR2. Genome analysis revealed B. velezensis ATR2 harbored a series of genes closely related to promoting plant growth and triggering plant immunity. Meanwhile, ten gene clusters involved in the biosynthesis of various secondary metabolites (surfactin, bacillomycin, fengycin, bacillibactin, bacilysin, difficidin, macrolactin, bacillaene, plantazolicin, and amylocyclicin) and two clusters encoding a putative lipopeptide and a putative phosphonate which might be explored as novel bioactive compounds were also present in the ATR2 genome. Moreover, B. velezensis ATR2 showed excellent antagonistic activities against multiple plant pathogenic bacteria, plant pathogenic fungi, human pathogenic bacteria, and human pathogenic fungus. B. velezensis ATR2 was also efficacious in control of aphids. The antagonistic compound from B. velezensis ATR2 against B.pumilus GR8 was purified and identified as bacillomycin D. In addition, B. velezensis ATR2 exhibited excellent biocontrol efficacy against ginger rhizome rot disease on ginger slices. These findings showed the potential of further applications of B. velezensis ATR2 as a biocontrol agent in agricultural diseases and pests management.

The FtcR-Like Protein ActR in Azorhizobium caulinodans ORS571 Is Involved in Bacterial Motility and Symbiosis With the Host Plant

Bacterial signal transduction pathways are important for a variety of adaptive responses to environment, such as two-component systems (TCSs). In this paper, we reported the characterization of a transcriptional regulator in Azorhizobium caulinodans ORS571, ActR, with an N-terminal receiver domain and one C-terminal OmpR/PhoB-type DNA binding domain. Sequence analysis showed that ActR shared a high similarity with FtcR regulator of Brucella melitensis 16M known to be involved in flagellar regulation. The structural gene of this regulator was largely distributed in Alphaproteobacteria, in particular in Rhizobiales and Rhodobacterales, and was located within clusters of genes related to motility functions. Furthermore, we studied the biological function of ActR in A. caulinodans grown at the free-living state or in association with Sesbania rostrata by constructing actR gene deletion mutant. In the free-living state, the bacterial flagellum and motility ability were entirely deleted, the expression of flagellar genes was downregulated; and the exopolysaccharide production, biofilm formation, and cell flocculation decreased significantly compared with those of the wild-type strain. In the symbiotic state, ΔactR mutant strain showed weakly competitive colonization and nodulation on the host plant. These results illustrated that FtcR-like regulator in A. caulinodans is involved in flagellar biosynthesis and provide bacteria with an effective competitive nodulation for symbiosis. These findings improved our knowledge of FtcR-like transcriptional regulator in A. caulinodans.

Bacillus velezensis: A Treasure House of Bioactive Compounds of Medicinal, Biocontrol and Environmental Importance

Bacillus velezensis gram-positive bacterium, is frequently isolated from diverse niches mainly soil, water, plant roots, and fermented foods. B. velezensis is ubiquitous, non-pathogenic and endospore forming. Being frequently isolated from diverse plant holobionts it is considered host adapted microorganism and recognized of high economic importance given its ability to promote plant growth under diverse biotic and abiotic stress conditions. Additionally, the species suppress many plant diseases, including bacterial, oomycete, and fungal diseases. It is also able after plant host root colonization to induce unique physiological situation of host plant called primed state. Primed host plants are able to respond more rapidly and/or effectively to biotic or abiotic stress. Moreover, B. velezenis have the ability to resist diverse environmental stresses and help host plants to cope with, including metal and xenobiotic stresses. Within species B. velezensis strains have unique abilities allowing them to adopt different life styles. Strain level abilities knowledge is warranted and could be inferred using the ever-expanding new genomes list available in genomes databases. Pangenome analysis and subsequent identification of core, accessory and unique genomes is actually of paramount importance to decipher species full metabolic capacities and fitness across diverse environmental conditions shaping its life style. Despite the crucial importance of the pan genome, its assessment among large number of strains remains sparse and systematic studies still needed. Extensive knowledge of the pan genome is needed to translate genome sequencing efforts into developing more efficient biocontrol agents and bio-fertilizers. In this study, a genome survey of B. velezensis allowed us to (a) highlight B. velezensis species boundaries and show that Bacillus suffers taxonomic imprecision that blurs the debate over species pangenome; (b) identify drivers of their successful acquisition of specific life styles and colonization of new niches; (c) describe strategies they use to promote plant growth and development; (d) reveal the unlocked strain specific orphan secondary metabolite gene clusters (biosynthetic clusters with corresponding metabolites unknown) that product identification is still awaiting to amend our knowledge of their putative role in suppression of pathogens and plant growth promotion, and (e) to describe a dynamic pangenome with a secondary metabolite rich accessory genome.

Bacillus velezensis 83 increases productivity and quality of tomato (Solanum lycopersicum L.): Pre and postharvest assessment

Bacillus spp. are well known plant growth promoting bacteria (PGPB) and biological control agents (BCA) due to their capacity to synthesize a wide variety of phytostimulant and antimicrobial compounds. B. velezensis 83 is a strain marketed in Mexico as a foliar biofungicide (Fungifree AB™) which has been used for biological control of five different genera of phytopathogenic fungi (Colletotrichum, Erysiphe, Botrytis, Sphaerotheca, Leveillula) in crops of agricultural importance such as mango, avocado, papaya, citrus, tomato, strawberry, blueberry, blackberry and cucurbits, among others. In this work, the potential of plant growth promotion of B. velezensis 83 was evaluated on different phenological stages of tomato plants as well as the biocontrol efficacy of B. velezensis 83 formulations (cells and/or metabolites) against B. cinerea infection on leaves and postharvest fruits. Greenhouse grown tomato plants inoculated with a high concentration (1 × 108 CFU/plant) of B. velezensis 83 yielded 254 tons/Ha•year of which the 64% was first quality tomato (≥100 g/fruit), while the control plants produced less than 184 tons/Ha•year with only 55% of first quality tomato. Additionally, in vitro assays carried out with leaves and fruits, shown that the B. velezensis 83 cells formulation had an efficacy of control of B. cinerea infection of ∼31% on leaves and ∼89% on fruits, while the metabolites formulation had an efficacy of control of less than 10%. Therefore, it was concluded that spores (not the metabolites) are the main antagonism factor of Fungifree AB™. The high effectivity of B. cinerea control on fruits by B. velezensis 83, opens the possibility for a postharvest use of this biofungicide.

The Role of Surfactin Production by Bacillus velezensis on Colonization, Biofilm Formation on Tomato Root and Leaf Surfaces and Subsequent Protection (ISR) against Botrytis cinerea

Many aspects regarding the role of lipopeptides (LPs) in bacterial interaction with plants are not clear yet. Of particular interest is the LP family of surfactin, immunogenic molecules involved in induced systemic resistance (ISR) and the bacterial colonization of plant surfaces. We hypothesize that the concentration of surfactin produced by a strain correlates directly with its ability to colonize and persist on different plant surfaces, which conditions its capacity to trigger ISR. We used two Bacillus velezensis strains (BBC023 and BBC047), whose antagonistic potential in vitro is practically identical, but not on plant surfaces. The surfactin production of BBC047 is 1/3 higher than that of BBC023. Population density and SEM images revealed stable biofilms of BBC047 on leaves and roots, activating ISR on both plant surfaces. Despite its lower surfactin production, strain BBC023 assembled stable biofilms on roots and activated ISR. However, on leaves only isolated, unstructured populations were observed, which could not activate ISR. Thus, the ability of a strain to effectively colonize a plant surface is not only determined through its production of surfactin. Multiple aspects, such as environmental stressors or compensation mechanisms may influence the process. Finally, the importance of surfactin lies in its impacts on biofilm formation and stable colonization, which finally enables its activity as an elicitor of ISR.

Pathogen Biocontrol Using Plant Growth-Promoting Bacteria (PGPR): Role of Bacterial Diversity

A vast microbial community inhabits in the rhizosphere, among which, specialized bacteria known as Plant Growth-Promoting Rhizobacteria (PGPR) confer benefits to host plants including growth promotion and disease suppression. PGPR taxa vary in the ways whereby they curtail the negative effects of invading plant pathogens. However, a cumulative or synergistic effect does not always ensue when a bacterial consortium is used. In this review, we reassess the disease-suppressive mechanisms of PGPR and present explanations and illustrations for functional diversity and/or stability among PGPR taxa regarding these mechanisms. We also provide evidence of benefits when PGPR mixtures, rather than individuals, are used for protecting crops from various diseases, and underscore the critical determinant factors for successful use of PGPR mixtures. Then, we evaluate the challenges of and limitations to achieving the desired outcomes from strain/species-rich bacterial assemblages, particularly in relation to their role for plant disease management. In addition, towards locating additive or synergistic outcomes, we highlight why and how the benefits conferred need to be categorized and quantified when different strains/species of PGPR are used in combinations. Finally, we highlight the critical approaches needed for developing PGPR mixtures with improved efficacy and stability as biocontrols for utilization in agricultural fields.

Cyclic siloxane biosurfactant-producing Bacillus cereus BS14 biocontrols charcoal rot pathogen Macrophomina phaseolina and induces growth promotion in Vigna mungo L

Rhizobacteria are vital component of soil-plant interfaces which helps in plant growth responses and disease management. Precisely, the role of biosurfactant production by rhizobacteria in biocontrol mechanisms is underscored. The current study explores the destructive effect of a biosurfactant-producing bacterium Bacillus cereus BS14 on fungal growth under in vitro experiments and showed in vivo reduction of disease severity in pulse crop Vigna mungo. In this study, B. cereus BS14 was observed as plant growth-promoting rhizobacterium (PGPR) based on abilities of production of phytohormone and HCN, phosphate solubilization and biocontrol of Macrophomina phaseolina. The purified biosurfactant from BS14 inhibited the fungal growth by arresting radially growing mycelia. Scanning electron microscope (SEM) study revealed deformities at cellular level in the mycelia of M. phaseolina. The biosurfactant of Bacillus BS14 was identified as cyclic siloxane in GC-MS spectroscopy and FT-IR spectroscopy analyses. In the pot trial studies, B. cereus BS14 proved its efficiency for the growth promotion of Vigna mungo and significantly reduced disease severity index. The present study concludes that biosurfactant of rhizobacterial origin and rhizobacteria can serve for biological control, improvement in crop production and agricultural sustainability. In future, it can be developed as biological control and biofertilizer formulations for legume crops, and commercialized for routine farming practices.

Whole Genome Sequence of Bacillus velezensis Strain GUMT319: A Potential Biocontrol Agent Against Tobacco Black Shank Disease

Phytophthora nicotianae causes black shank, a serious soil-borne disease, in tobacco. In this study, the Bacillus strain GUMT319 was isolated from the rhizosphere of healthy tobacco plants grown in a field in Guizhou with a high incidence of tobacco black shank. Genome sequencing revealed that GUMT319 contained a single circular chromosome 3,940,023 bp in length, with 4,053 predicted genes and an average GC content of 46.6%. Based on phylogenomic analyses, GUMT319 was designated as Bacillus velezensis. The genome of GUMT319 contained more than 60 genes and 13 gene clusters that have previously been found to be active in antifungal mechanisms, biofilm formation, and chemotaxis motility. Additionally, confocal laser scanning microscopy and scanning electron microscopy showed that GUMT319 formed a spatially organized biofilm in vivo. In addition, lauric acid negatively regulated biofilm formation. This is the first study to report that nicotine in tobacco root exudates was a chemoattractant for biocontrol Bacillus strains. In this study, we identified new interactions between beneficial microorganisms and tobacco roots in the rhizosphere. Moreover, dual culture tests in vitro showed that GUMT319 inhibited the growth of P. nicotianae and also displayed inhibitory effects against eight other plant pathogens, namely, Colletotrichum scovillei, Colletotrichum capsici, Fusarium carminascens, Sclerotinia sclerotiorum, Alternaria alternata, Phomopsis sp., Phyllosticta sorghina, and Exserohilum turcicum. Furthermore, GUMT319 exhibited > 70% control efficiency against tobacco black shank in field experiments conducted in 2018–2020. Thus, GUMT319 was more effective in controlling the incidence of tobacco black shank than other treatments including fungicide application. Overall, these results suggested that GUMT319 (B. velezensis) could be used as a potential biocontrol agent against tobacco black shank.

Harnessing PGPR inoculation through exogenous foliar application of salicylic acid and microbial extracts for improving rice growth

Plant-growth-promoting rhizobacteria (PGPR) should effectively colonize along the plant root to enhance the plant and soil health. The present investigation aims to improve the PGPR-mediated plant health benefits through above-ground foliar management. A green fluorescent protein-tagged PGPR strain, Pseudomonas chlororaphis (ZSB15-M2) was inoculated in a nonautoclaved agricultural soil before rice culturing. Salicylic acid and cell extracts of Corynebacterium glutamicum and Saccharomyces cerevisiae as a supply of hormonal and inducer compounds were applied on the foliage of the 10-days-old rice plants and subsequently observed the colonizing ability of ZSB15-M2. The cell extracts of Corynebacteria and yeast showed a 100-fold increase in the ZSB15-M2 population in the rhizosphere of rice, whereas salicylic acid had a 10-fold increase in relation to mock control. The rice root exudates collected after the spraying of salicylic acid and microbial extracts showed significantly enhanced release of total carbon, total protein, total sugar, total amino nitrogen, total nitrogen, and phenol content. In vitro assays revealed that these root exudates collected after exogenous spray of these chemicals enhanced the chemotactic motility and biofilm formation of ZSB15-M2 compared to the control plant's root exudate. Metabolomic analysis of root exudates collected from these rice plants by gas chromatography-mass spectrometry revealed that the Corynebacteria and yeast cell extracts enhanced the divergence of metabolites of rice root exudate. Further, due to these cumulative effects in the rice rhizosphere, the total chlorophyll, total protein, total nitrogen, and total phosphorus of rice were significantly improved. These observations provide insights into the rhizosphere functioning of rice plants as modulated by above-ground treatments with improved colonization of inoculant strains as well as the plant growth.

A Crosstalk Between Brachypodium Root Exudates, Organic Acids, and Bacillus velezensis B26, a Growth Promoting Bacterium

Plant growth-promoting rhizobacteria (PGPR) are associated with plant roots and use organic compounds that are secreted from root exudates as food and energy source. Root exudates can chemoattract and help bacteria to colonize the surface of plant roots by inducing chemotactic responses of rhizospheric bacteria. In this study, we show that root colonization of Brachypodium distachyon by Bacillus velezensis strain B26 depends on several factors. These include root exudates, organic acids, and their biosynthetic genes, chemotaxis, biofilm formation and the induction of biofilm encoding genes. Analysis of root exudates by GC-MS identified five intermediates of the TCA cycle; malic, fumaric, citric, succinic, oxaloacetic acids, and were subsequently evaluated. The strongest chemotactic responses were induced by malic, succinic, citric, and fumaric acids. In comparison, the biofilm formation was induced by all organic acids with maximal induction by citric acid. Relative to the control, the individual organic acids, succinic and citric acids activated the epsD gene related to EPS biofilm, and also the genes encoding membrane protein (yqXM) and hydrophobin component (bslA) of the biofilm of strain B26. Whereas epsA and epsB genes were highly induced genes by succinic acid. Similarly, concentrated exudates released from inoculated roots after 48 h post-inoculation also induced all biofilm-associated genes. The addition of strain B26 to wild type and to icdh mutant line led to a slight induction but not biologically significant relative to their respective controls. Thus, B26 has no effect on the expression of the ICDH gene, both in the wild type and the mutant backgrounds. Our results indicate that root exudates and individual organic acids play an important role in selective recruitment and colonization of PGPR and inducing biofilm. The current study increases the understanding of molecular mechanisms behind biofilm induction by organic acids.

Bacillus velezensis 83 a bacterial strain from mango phyllosphere, useful for biological control and plant growth promotion

Bacillus velezensis 83 was isolated from mango tree phyllosphere of orchards located in El Rosario, Sinaloa, México. The assessment of this strain as BCA (biological control agent), as well as PGPB (plant growth-promoting bacteria), were demonstrated through in vivo and in vitro assays. In vivo assays showed that B. velezensis 83 was able to control anthracnose (Kent mangoes) as efficiently as chemical treatment with Captan 50 PH™ or Cupravit hidro™. The inoculation of B. velezensis 83 to the roots of maize seedlings yielded an increase of 12% in height and 45% of root biomass, as compared with uninoculated seedlings. In vitro co-culture assays showed that B. velezensis 83 promoted Arabidopsis thaliana growth (root and shoot biomass) while, under the same experimental conditions, B. velezensis FZB42 (reference strain) had a suppressive effect on plant growth. In order to characterize the isolated strain, the complete genome sequence of B. velezensis 83 is reported. Its circular genome consists of 3,997,902 bp coding to 3949 predicted genes. The assembly and annotation of this genome revealed gene clusters related with plant-bacteria interaction and sporulation, as well as ten secondary metabolites biosynthetic gene clusters implicated in the biological control of phytopathogens. Despite the high genomic identity (> 98%) between B. velezensis 83 and B. velezensis FZB42, they are phenotypically different. Indeed, in vitro production of compounds such as surfactin and bacillomycin D (biocontrol activity) and γ-PGA (biofilm component) is significantly different between both strains.

Secondary metabolites from plant-associated Pseudomonas are overproduced in biofilm

Plant rhizosphere soil houses complex microbial communities in which microorganisms are often involved in intraspecies as well as interspecies and inter-kingdom signalling networks. Some members of these networks can improve plant health thanks to an important diversity of bioactive secondary metabolites. In this competitive environment, the ability to form biofilms may provide major advantages to microorganisms. With the aim of highlighting the impact of bacterial lifestyle on secondary metabolites production, we performed a metabolomic analysis on four fluorescent Pseudomonas strains cultivated in planktonic and biofilm colony conditions. The untargeted metabolomic analysis led to the detection of hundreds of secondary metabolites in culture extracts. Comparison between biofilm and planktonic conditions showed that bacterial lifestyle is a key factor influencing Pseudomonas metabolome. More than 50% of the detected metabolites were differentially produced according to planktonic or biofilm lifestyles, with the four Pseudomonas strains overproducing several secondary metabolites in biofilm conditions. In parallel, metabolomic analysis associated with genomic prediction and a molecular networking approach enabled us to evaluate the impact of bacterial lifestyle on chemically identified secondary metabolites, more precisely involved in microbial interactions and plant-growth promotion. Notably, this work highlights the major effect of biofilm lifestyle on acyl-homoserine lactone and phenazine production in P. chlororaphis strains.

Agrobacterium tumefaciens C58 presence affects Bacillus velezensis 32a ecological fitness in the tomato rhizosphere

The persistence of pathogenic Agrobacterium strains as soil-associated saprophytes may cause an inconsistency in the efficacy of the biocontrol inoculants under field condition. The study of the interaction occurring in the rhizosphere between the beneficial and the pathogenic microbes is thus interesting for the development of effective biopesticides for the management of crown gall disease. However, very little is still known about the influence of these complex interactions on the biocontrol determinants of beneficial bacteria, especially Bacillus strains. This study aimed to evaluate the effect of the soil borne pathogen Agrobacterium tumefaciens C58 on root colonization and lipopeptide production by Bacillus velezensis strain 32a during interaction with tomato plants. Results show that the presence of A. tumefaciens C58 positively impacted the root colonization level of the Bacillus strain. However, negative impact on surfactin production was observed in Agrobacterium-treated seedling, compared with control. Further investigation suggests that these modulations are due to a modified tomato root exudate composition during the tripartite interaction. Thus, this work contributes to enhance the knowledge on the impact of interspecies interaction on the ecological fitness of Bacillus cells living in the rhizosphere.

Crop Protection against Botrytis cinerea by Rhizhosphere Biological Control Agent Bacillus velezensis XT1

This study aims to evaluate the use of Bacillus velezensis strain XT1 as a plant growth-promoting rhizobacterium (PGPR) and biocontrol agent against B. cinerea in tomato and strawberry plants. Foliar and radicular applications of strain XT1 increased plant total biomass as compared to the control and B. cinerea-infected plants, with root applications being, on the whole, the most effective mode of treatment. Applications of the bacterium were found to reduce infection parameters such as disease incidence and severity by 50% and 60%, respectively. We analyzed stress parameters and phytohormone content in order to evaluate the capacity of XT1 to activate the defense system through phytohormonal regulation. Overall, the application of XT1 reduced oxidative damage, while the H₂O₂ and malondialdehyde (MDA) content was lower in XT1-treated and B. cinerea-infected plants as compared to non-XT1-treated plants. Moreover, treatment with XT1 induced callose deposition, thus boosting the response to pathogenic infection. The results of this study suggest that the signaling and activation pathways involved in defense mechanisms are mediated by jasmonic acid (JA) and ethylene hormones, which are induced by preventive treatment with XT1. The study also highlights the potential of preventive applications of strain XT1 to activate defense mechanisms in strawberry and tomato plants through hormone regulation.

Plant Growth Promotion Abilities of Phylogenetically Diverse Mesorhizobium Strains: Effect in the Root Colonization and Development of Tomato Seedlings

Mesorhizobium contains species widely known as nitrogen-fixing bacteria with legumes, but their ability to promote the growth of non-legumes has been poorly studied. Here, we analyzed the production of indole acetic acid (IAA), siderophores and the solubilization of phosphate and potassium in a collection of 24 strains belonging to different Mesorhizobium species. All these strains produce IAA, 46% solubilized potassium, 33% solubilize phosphate and 17% produce siderophores. The highest production of IAA was found in the strains Mesorhizobiumciceri CCANP14 and Mesorhizobiumtamadayense CCANP122, which were also able to solubilize potassium. Moreover, the strain CCANP14 showed the maximum phosphate solubilization index, and the strain CCANP122 was able to produce siderophores. These two strains were able to produce cellulases and cellulose and to originate biofilms in abiotic surfaces and tomato root surface. Tomato seedlings responded positively to the inoculation with these two strains, showing significantly higher plant growth traits than uninoculated seedlings. This is the first report about the potential of different Mesorhizobium species to promote the growth of a vegetable. Considering their use as safe for humans, animals and plants, they are an environmentally friendly alternative to chemical fertilizers for non-legume crops in the framework of sustainable agriculture.

Genetic, Epigenetic and Phenotypic Diversity of Four Bacillus velezensis Strains Used for Plant Protection or as Probiotics

Bacillus velezensis strains are applied as ecologically safe biopesticides, plant growth promoting rhizobacteria (PGPR), and in veterinary probiotics. They are abundant in various environments including soil, plants, marine habitats, the intestinal micro-flora, etc. The mechanisms underlying this adaptive plasticity and bioactivity are not well understood, nor is it clear why several strains outperform other same species isolates by their bioactivities. The main objective of this work was to demonstrate versatility of bioactivities and lifestyle strategies of the selected B. velezensis strains suitable to serve as model organisms in future studies. Here, we performed a comparative study of newly sequenced genomes of four B. velezensis isolates with distinct phenotypes and isolation origin, which were assessed by RNA sequencing under the effect of root exudate stimuli and profiled by epigenetic modifications of chromosomal DNA. Among the selected strains, UCMB5044 is an oligotrophic PGPR strain adapted to nutrient poor desert soils. UCMB5113 and At1 are endophytes that colonize plants and require nutrient rich media. In contrast, the probiotic strain, UCMB5007, is a copiotroph, which shows no propensity to colonize plants. PacBio and Illumina sequencing approaches were used to generate complete genome assemblies, tracing epigenetic modifications, and determine gene expression profiles. All sequence data was deposited at NCBI. The strains, UCMB5113 and At1, show 99% sequence identity and similar phenotypes despite being isolated from geographically distant regions. UCMB5007 and UCMB5044 represent another group of organisms with almost identical genomes but dissimilar phenotypes and plant colonization propensity. The two plant associated strains, UCMB5044 and UCMB5113, share 398 genes putatively associated with root colonization, which are activated by exposure to maize root exudates. In contrast, UCMB5007 did not respond to root exudate stimuli. It was hypothesized that alterations in the global methylation pattern and some other epigenetic modifications enable adaptation of strains to different habitats and therefore may be of importance in terms of the biotechnological applicability of these bacteria. Contrary, the ability to grow on root exudates as a sole source of nutrients or a strong antagonism against phytopathogens showed by the strains in vitro cannot be considered as good predictors of PGPR activities.