Screening, plant growth promotion and root colonization pattern of two rhizobacteria (Pseudomonas fluorescens Ps006 and Bacillus amyloliquefaciens Bs006) on banana cv. Williams (Musa acuminata Colla)

Endophytic microbial diversity associated with commercial cultivar and crop wild relative banana variety could provide clues for microbial community management

Endophytes, microorganisms inhabiting internal plant tissues, play a pivotal role in plant growth and disease resistance. Moreover, previous studies have established that Musa plants derive disease protective functions from their microbiome. Notably, one of the crop wild relatives of banana, the Calcutta 4 variety, exhibits resistance to various phytopathogens such as Pseudocercospora fijiensis (P. fijiensis), while the Williams commercial cultivar (cv.) is highly susceptible. Therefore, this study aims primarily to characterize and compare the endophytic microbiota composition of Calcutta 4 and Williams banana plants when grown sympatrically. Alongside, differences in endophytic microbiome between plant sections (shoot or roots), growth phases (in vitro or greenhouse) and fitness factors such as the addition of plant growth-promoting bacteria Bacillus subtilis EA-CB0575 (T2 treatment) or infection by P. fijiensis (T3 treatment) were examined. Both culture-dependent and -independent techniques were used to evaluate these differences and assess the culturability of banana endophytes under varying conditions. Microbial cultures resulted in 331 isolates distributed across 54 genera when all treatments were evaluated, whereas 16 S sequencing produced 9510 ASVs assigned in 1456 genera. Alpha and beta diversity exhibited significant differences based on plant section, with an increase in phylogenetic diversity observed in plants with pathogen infection (T3) compared to control plants (T1). Additionally, four differentially abundant genera associated with nitrogen metabolism were identified in T3 plants and seven genera showed differential abundance when comparing varieties. When culture-dependent and -independent methods were compared, it was found that isolates represented 3.7 % of the genera detected by culture-independent methods, accounting for 12-41 % of the total data depending on the treatment. These results are crucial for proposing management strategies derived from crop wild relatives to enhance the resilience of susceptible commercial varieties against fitness factors affecting crop development. Additionally, they help to decipher the pathogenic effects of P. fijiensis in banana plants and advance the understanding of how plant domestication influences the endosphere.

Assessment of Plant Growth Promotion Potential of Endophytic Bacterium B. subtilis KU21 Isolated from Rosmarinus officinalis

The current study aimed to evaluate the plant growth-promoting (PGP) potential of endophytic strain Bacillus subtilis KU21 isolated from the roots of Rosmarinus officinalis. The strain exhibited multiple traits of plant growth promotion viz., phosphate (P) solubilization, nitrogen fixation, indole-3-acetic acid (IAA), siderophore, hydrogen cyanide (HCN), lytic enzymes production, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. The isolate also exhibited antagonistic activity against phytopathogenic fungi, i.e., Fusarium oxysporum, Fusarium graminiarum, and Rhizoctonia solani. The P-solubilization activity of B. subtilis KU21 was further elucidated via detection of glucose dehydrogenase (gdh) gene involved in the production of gluconic acid which is responsible for P-solubilization. Further, B. subtilis KU21 was evaluated for in vivo growth promotion studies of tomato (test crop) under net house conditions. A remarkable increase in seed germination, plant growth parameters, nutrient acquisition, and soil quality parameters (NPK) was observed in B. subtilis KU21-treated plants over untreated control. Hence, the proposed module could be recommended for sustainable tomato production in the Northwest Himalayan region without compromising soil health and fertility.

Investigating the in vivo biocontrol and growth-promoting efficacy of Bacillus sp. and Pseudomonas fluorescens against olive knot disease

Olive knot disease, caused by Pseudomonas savastanoi, poses a significant threat to olive cultivation, necessitating sustainable alternatives to conventional chemical control. This study investigates the biocontrol effectiveness of Bacillus sp. (Og2) and Pseudomonas fluorescens (Oq5), alone and combined, against olive knot disease. Olive plants were sprayed with 5 ml of the bacteria until uniformly wet, with additional application to the soil surface. Pathogen injection occurred 24 h later. The results revealed that treating plants with a combination of both bacteria provided the highest reduction in disease severity (89.58 %), followed by P. fluorescens alone (69.38 %). Significant improvements were observed in shoot height, particularly with the combination of Bacillus sp. and P. fluorescens. The root length of olive seedlings treated with P. fluorescens and Bacillus sp., either alone or in combination, was significantly longer compared to the control and pathogen-treated seedlings. In terms of root dry weight, the most effective treatments were treated with P. fluorescens was the highest (82.94 g) among all treatments followed by the combination of both isolates with seedlings inoculated with P. savastanoi. These findings underscore the potential of Bacillus sp. and Pseudomonas fluorescens as effective biocontrol agents against olive knot disease and promoting olive seedlings growth, providing a sustainable and environmentally friendly approach to disease management.

Combined application of microbial inoculant and kelp-soaking wastewater promotes wheat seedlings growth and improves structural diversity of rhizosphere microbial community

Industrial processing of kelp generates large amounts of kelp-soaking wastewater (KSW), which contains a large amount of nutrient-containing substances. The plant growth-promoting effect might be further improved by combined application of growth-promoting bacteria and the nutrient-containing KSW. Here, a greenhouse experiment was conducted to determine the effect of the mixture of KSW and Bacillus methylotrophicus M4-1 (MS) vs. KSW alone (SE) on wheat seedlings, soil properties and the microbial community structure in wheat rhizosphere soil. The available potassium, available nitrogen, organic matter content and urease activity of MS soil as well as the available potassium of the SE soil were significantly different (p < 0.05) from those of the CK with water only added, increased by 39.51%, 36.25%, 41.61%, 80.56% and 32.99%, respectively. The dry and fresh weight of wheat seedlings from MS plants increased by 166.17% and 50.62%, respectively, while plant height increased by 16.99%, compared with CK. Moreover, the abundance and diversity of fungi in the wheat rhizosphere soil were significantly increased (p < 0.05), the relative abundance of Ascomycetes and Fusarium spp. decreased, while the relative abundance of Bacillus and Mortierella increased. Collectively, the combination of KSW and the plant growth-promoting strain M4-1 can promote wheat seedlings growth and improve the microecology of rhizosphere microorganisms, thereby solving the problems of resource waste and environmental pollution, ultimately turning waste into economic gain.

Role of an antagonistic bacterium, Bacillus subtilis PE7, in growth promotion of netted melon (Cucumis melo L. var. reticulatus Naud.)

The aim of this study was to determine the plant growth-promoting effect of Bacillus subtilis PE7 on growth of melon plants. B. subtilis PE7 isolated from kimchi was identified based on colonial and microscopic morphology along with analyses of 16S rRNA and pycA gene sequences. Strain PE7 showed different levels of inhibition on phytopathogens and was able to grow at variable temperatures and pH values. Strain PE7 had the ability to produce siderophores, indole-3-acetic acid (IAA), ammonia, exopolysaccharides, and 1-aminocyclopropane-1-carboxylic acid deaminase, as well as solubilize insoluble phosphate and zinc. The IAA secretion of strain PE7 showed a concentration-dependent pattern based on the concentration of l-tryptophan supplemented in the fertilizer-based culture medium. The LC-MS analysis indicates the presence of IAA in the culture filtrate of strain PE7. Treatment of the B. subtilis PE7 culture containing different metabolites, mainly IAA, significantly promoted melon growth in terms of higher growth parameters and greater plant nutrient contents compared to treatments with the culture without IAA, fertilizer, and water. The cells of B. subtilis PE7 attached to and firmly colonized the roots of the bacterized melon plants. Based on our results, B. subtilis PE7 can be utilized as a potential microbial fertilizer to substitute chemical fertilizers in sustainable agriculture.

Identification and Characterization of Beneficial Soil Microbial Strains for the Formulation of Biofertilizers Based on Native Plant Growth-Promoting Microorganisms Isolated from Northern Mexico

Plant growth-promoting microorganisms (PGPM) benefit plant health by enhancing plant nutrient-use efficiency and protecting plants against biotic and abiotic stresses. This study aimed to isolate and characterize autochthonous PGPM from important agri-food crops and nonagricultural plants to formulate biofertilizers. Native microorganisms were isolated and evaluated for PGP traits (K, P, and Zn solubilization, N2-fixation, NH3-, IAA and siderophore production, and antifungal activity against Fusarium oxysporum). Isolates were tested on radish and broccoli seedlings, evaluating 19 individual isolates and 12 microbial consortia. Potential bacteria were identified through DNA sequencing. In total, 798 bacteria and 209 fungi were isolated. Isolates showed higher mineral solubilization activity than other mechanisms; 399 bacteria and 156 fungi presented mineral solubilization. Bacteria were relevant for nitrogen fixation, siderophore, IAA (29-176 mg/L), and ammonia production, while fungi for Fusarium growth inhibition (40-69%). Twenty-four bacteria and eighteen fungi were selected for their PGP traits. Bacteria had significantly (ANOVA, p < 0.05) better effects on plants than fungi; treatments improved plant height (23.06-51.32%), leaf diameter (25.43-82.91%), and fresh weight (54.18-85.45%) in both crops. Most potential species belonged to Pseudomonas, Pantoea, Serratia, and Rahnella genera. This work validated a high-throughput approach to screening hundreds of rhizospheric microorganisms with PGP potential isolated from rhizospheric samples.

Towards further understanding the applications of endophytes: enriched source of bioactive compounds and bio factories for nanoparticles

The most significant issues that humans face today include a growing population, an altering climate, an growing reliance on pesticides, the appearance of novel infectious agents, and an accumulation of industrial waste. The production of agricultural goods has also been subject to a great number of significant shifts, often known as agricultural revolutions, which have been influenced by the progression of civilization, technology, and general human advancement. Sustainable measures that can be applied in agriculture, the environment, medicine, and industry are needed to lessen the harmful effects of the aforementioned problems. Endophytes, which might be bacterial or fungal, could be a successful solution. They protect plants and promote growth by producing phytohormones and by providing biotic and abiotic stress tolerance. Endophytes produce the diverse type of bioactive compounds such as alkaloids, saponins, flavonoids, tannins, terpenoids, quinones, chinones, phenolic acids etc. and are known for various therapeutic advantages such as anticancer, antitumor, antidiabetic, antifungal, antiviral, antimicrobial, antimalarial, antioxidant activity. Proteases, pectinases, amylases, cellulases, xylanases, laccases, lipases, and other types of enzymes that are vital for many different industries can also be produced by endophytes. Due to the presence of all these bioactive compounds in endophytes, they have preferred sources for the green synthesis of nanoparticles. This review aims to comprehend the contributions and uses of endophytes in agriculture, medicinal, industrial sectors and bio-nanotechnology with their mechanism of action.

Profiling of Antimicrobial Metabolites Synthesized by the Endophytic and Genetically Amenable Biocontrol Strain Bacillus velezensis DMW1

The genus Bacillus is one of the most important genera for the biological control of plant diseases that are caused by various phytopathogens. The endophytic Bacillus strain DMW1 was isolated from the inner tissues of potato tubers and exhibited strong biocontrol activity. Based on its whole-genome sequence, DMW1 belongs to the Bacillus velezensis species, and it is similar to the model strain B. velezensis FZB42. 12 secondary metabolite biosynthetic gene clusters (BGCs), including two unknown function BGCs, were detected in the DMW1 genome. The strain was shown to be genetically amenable, and seven secondary metabolites acting antagonistically against plant pathogens were identified by a combined genetic and chemical approach. Strain DMW1 did significantly improve the growth of tomato and soybean seedlings, and it was able to control the Phytophthora sojae and Ralstonia solanacearum that were present in the plant seedlings. Due to these properties, the endophytic strain DMW1 appears to be a promising candidate for comparative investigations performed together with the Gram-positive model rhizobacterium FZB42, which is only able to colonize the rhizoplane. IMPORTANCE Phytopathogens are responsible for the wide spread of plant diseases as well as for great losses of crop yields. At present, the strategies used to control plant disease, including the development of resistant cultivars and chemical control, may become ineffective due to the adaptive evolution of pathogens. Therefore, the use of beneficial microorganisms to deal with plant diseases attracts great attention. In the present study, a new strain DMW1, belonging to the species B. velezensis, was discovered with outstanding biocontrol properties. It showed plant growth promotion and disease control abilities that are comparable with those of B. velezensis FZB42 under greenhouse conditions. According to a genomic analysis and a bioactive metabolites analysis, genes that are responsible for promoting plant growth were detected, and metabolites with different antagonistic activities were identified. Our data provide a basis for DMW1 to be further developed and applied as a biopesticide, which is similar to the closely related model strain FZB42.

Physiological and molecular insight of microbial biostimulants for sustainable agriculture

Increased food production to cater the need of growing population is one of the major global challenges. Currently, agro-productivity is under threat due to shrinking arable land, increased anthropogenic activities and changes in the climate leading to frequent flash floods, prolonged droughts and sudden fluctuation of temperature. Further, warm climatic conditions increase disease and pest incidences, ultimately reducing crop yield. Hence, collaborated global efforts are required to adopt environmentally safe and sustainable agro practices to boost crop growth and productivity. Biostimulants appear as a promising means to improve growth of plants even under stressful conditions. Among various categories of biostimulants, microbial biostimulants are composed of microorganisms such as plant growth-promoting rhizobacteria (PGPR) and/or microbes which stimulate nutrient uptake, produce secondary metabolites, siderophores, hormones and organic acids, participate in nitrogen fixation, imparts stress tolerance, enhance crop quality and yield when applied to the plants. Though numerous studies convincingly elucidate the positive effects of PGPR-based biostimulants on plants, yet information is meagre regarding the mechanism of action and the key signaling pathways (plant hormone modulations, expression of pathogenesis-related proteins, antioxidants, osmolytes etc.) triggered by these biostimulants in plants. Hence, the present review focuses on the molecular pathways activated by PGPR based biostimulants in plants facing abiotic and biotic challenges. The review also analyses the common mechanisms modulated by these biostimulants in plants to combat abiotic and biotic stresses. Further, the review highlights the traits that have been modified through transgenic approach leading to physiological responses akin to the application of PGPR in the target plants.

Effect of the application or coating of PGPR-based biostimulant on the growth, yield and nutritional status of maize in Benin

Biotechnology proposes various ecological approaches to control climatic constraints, soil fertility and plant nutrition using biological products, such as biostimulants to achieve a healthy and environment-friendly agriculture. The aim of this study was to compare the effect of biostimulant-coated maize seed and biostimulant application on the growth, yield and nutritional status of maize in Benin. The trials were set up with 100 producers spread over the whole of Benin. The experimental design was a block of three treatments with 11 replicates per Research-Development (R-D) sites. The maize varieties 2000 SYNEE-W BENIN and TZL COMP 4-W BENIN were used. The best growth (height, stem diameter and leaf area) and yield performances (thousand grains weight and grains yield) were obtained by treatments T2 (Application of biostimulant + ½ NPK-Urea) and T3 (Seed coating with biostimulant + ½ NPK-Urea) compared to the farmers' practice (T1). A significant difference was observed between the different treatments for height, leaf area, 1000 grains weight and maize-grain yield. From one Research-Development site to another, a significant difference was also observed for all parameters. The treatment- Research-Development site interaction was also significant in most areas. The applied or coated biostimulant improved the uptake of nitrogen, phosphorus and especially potassium with higher significant difference compared to the recommended dose of mineral fertilizer. The two techniques of using the biostimulant combined with the half-dose of mineral fertilizer gave the better growth, yield and nutritional status compared to the farmers' practice in all areas study. This biostimulant can be used to ensure food security and sustainable agriculture in Benin.

Phytomicrobiome communications: Novel implications for stress resistance in plants

The agricultural sector is a foremost contributing factor in supplying food at the global scale. There are plethora of biotic as well as abiotic stressors that act as major constraints for the agricultural sector in terms of global food demand, quality, and security. Stresses affect rhizosphere and their communities, root growth, plant health, and productivity. They also alter numerous plant physiological and metabolic processes. Moreover, they impact transcriptomic and metabolomic changes, causing alteration in root exudates and affecting microbial communities. Since the evolution of hazardous pesticides and fertilizers, productivity has experienced elevation but at the cost of impeding soil fertility thereby causing environmental pollution. Therefore, it is crucial to develop sustainable and safe means for crop production. The emergence of various pieces of evidence depicting the alterations and abundance of microbes under stressed conditions proved to be beneficial and outstanding for maintaining plant legacy and stimulating their survival. Beneficial microbes offer a great potential for plant growth during stresses in an economical manner. Moreover, they promote plant growth with regulating phytohormones, nutrient acquisition, siderophore synthesis, and induce antioxidant system. Besides, acquired or induced systemic resistance also counteracts biotic stresses. The phytomicrobiome exploration is crucial to determine the growth-promoting traits, colonization, and protection of plants from adversities caused by stresses. Further, the intercommunications among rhizosphere through a direct/indirect manner facilitate growth and form complex network. The phytomicrobiome communications are essential for promoting sustainable agriculture where microbes act as ecological engineers for environment. In this review, we have reviewed our building knowledge about the role of microbes in plant defense and stress-mediated alterations within the phytomicrobiomes. We have depicted the defense biome concept that infers the design of phytomicrobiome communities and their fundamental knowledge about plant-microbe interactions for developing plant probiotics.

The core bacterial microbiome of banana (Musa spp.)

BACKGROUND

Bananas (Musa spp.) are a globally significant crop and are severely afflicted by diseases for which there are no effective chemical controls. Banana microbiomes may provide novel solutions to these constraints but are difficult to manage due to their high diversity and variability between locations. Hence 'common core' taxa, which are a subset of the microbiome that frequent all, or most, individuals of a host species, represent logical targets for the development of microbiome management approaches. Here, we first performed a pot experiment to characterise the effects of two factors that are likely to differ between farms (viz. edaphic conditions and host genotype) on bacterial diversity in bulk soil and seven plant compartments. From this experiment, we created shortlisted core 'candidates' that were then refined using a survey of 52 field-grown Musa spp. We confirmed the importance of the core through network analysis and by comparing the sequences of our core taxa with those reported in 22 previous studies.

RESULTS

Diversity was found to differ between plant compartments and soils, but not genotypes. Therefore, we identified populations that were frequent across most plants irrespective of the soil in which they were grown. This led to the selection of 36 'common core' bacteria, that represented 65-95% of the dominant taxa in field-grown plants and were identified as highly interconnected 'hubs' using network analysis - a characteristic shown to be indicative of microbes that influence host fitness in studies of other plants. Lastly, we demonstrated that the core taxa are closely related to banana-associated bacteria observed on five other continents.

CONCLUSIONS

Our study provides a robust list of common core bacterial taxa for Musa spp. Further research may now focus on how changes in the frequencies and activities of these most persistent taxa influence host fitness. Notably, for several of our core taxa, highly similar populations have already been isolated in previous studies and may be amenable to such experimentation. This contribution should help to accelerate the development of effective Musa spp. microbiome management practices.

Halotolerant rhizobacteria isolated from a mangrove forest alleviate saline stress in Musa acuminata cv. Berangan

Saline soils resulting from anthropogenic activity and climate change present a challenge to future food security. Towards addressing this, we isolated and characterized halotolerant bacteria from a Malaysian mangrove forest, and explored their effect on morpho-physiological and biochemical parameters of banana plantlets under salt stress. A total of 88 rhizobacterial and 16 endophytic bacterial isolates collected from the roots and rhizosphere of Rhizophora apiculata, Avicennia alba and Sonneratia alba, were found to tolerate up to 400 mM of sea salt. Based on best performance in multiple plant growth traits, three rhizobacterial strains RB1, RB3 and RB4 and three endophytic bacterial strains EB1, EB2 and EB3 were used for further analysis. The rhizobacterial strains were identified as Bacillus sp. and endophytic bacteria as Pseudomonas sp. based on 16 S rRNA gene sequence. SEM observation confirmed colonization of each strain on banana plantlet roots. When colonized plantlets were subjected to 90 mM salt and compared to uninoculated (control) and mock inoculated plants, improved plant growth was observed with each of the strains, especially with bacterial strains EB3 and RB3. Biochemical analysis of plantlets revealed that root colonization with EB3 and RB3 enhanced levels of plant chlorophyll (> 5-fold), carotenoid (> 2.85-fold) and proline (2.6-fold and 2.3-fold), while plantlets also showed reduced MDA content (0.45-fold and 0.51-fold), significantly reduced generation of ROS (0.23-fold and 0.47-fold) and lower levels of electrolyte leakage (0.77 and 0.51-fold). Antioxidant enzymes also showed enhanced activity with EB3 and RB3. Our results indicate that these halotolerant Bacillus and Pseudomonas strains from the mangrove have multifunctional plant growth promoting activity and can reduce salt stress in bananas. This data provides a reference for exploring halotolerant microbes from hypersaline environments to overcome salt stress in plants.

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.

Metabolic properties, gene functions, and biosafety analysis reveal the action of three rhizospheric plant growth-promoting bacteria of Jujuncao (Pennisetum giganteum)

This study aimed to identify the specific genes associated with plant growth promotion and cadmium tolerance in three bacteria strains associated with Pennisetum giganteum as well as to determine their biosafety levels in their potential use as biofertilizers for promoting plant growth and phytoremediation activities. The plant growth-promoting (PGP) abilities of Enterobacter cloacae strain RCB980 (A3), Klebsiella pneumonia strain kpa (A4), and Klebsiella sp. strain XT-2 (A7) were determined by a growth promotion trial and through testing for PGP traits such as 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase enzyme production, phosphorus solubilization, siderophore synthesis, and indole-3 acetic acid (IAA) production. The genes that potentially contribute to the beneficial activities of these three strains were identified through an analysis of their genomes. To establish the biosafety of the candidate PGPB, a pathological study was undertaken whereby 20 Kunming mice were injected intraperitoneally to study and analyze the effects of the strains on growth and lung paraffin sections of the mice. The strains had no obvious toxicity effect on the tested mice and were therefore not considered as highly virulent strains. These strains are thus considered non-toxic, safe, and highly recommended for use in environmental remediation strategies and agricultural production.

Biohardening of Banana cv. Karpooravalli (ABB; Pisang Awak) With Bacillus velezensis YEBBR6 Promotes Plant Growth and Reprograms the Innate Immune Response Against Fusarium oxysporum f.sp. cubense

Induction of innate immune response and growth promotion in banana by B. velezensis against Foc.

Assessment of Bacterial Inoculant Delivery Methods for Cereal Crops

Despite growing evidence that plant growth-promoting bacteria can be used to improve crop vigor, a comparison of the different methods of delivery to determine which is optimal has not been published. An optimal inoculation method ensures that the inoculant colonizes the host plant so that its potential for plant growth-promotion is fully evaluated. The objective of this study was to compare the efficacy of three seed coating methods, seedling priming, and soil drench for delivering three bacterial inoculants to the sorghum rhizosphere and root endosphere. The methods were compared across multiple time points under axenic conditions and colonization efficiency was determined by quantitative polymerase chain reaction (qPCR). Two seed coating methods were also assessed in the field to test the reproducibility of the greenhouse results under non-sterile conditions. In the greenhouse seed coating methods were more successful in delivering the Gram-positive inoculant (Terrabacter sp.) while better colonization from the Gram-negative bacteria (Chitinophaga pinensis and Caulobacter rhizosphaerae) was observed with seedling priming and soil drench. This suggested that Gram-positive bacteria may be more suitable for the seed coating methods possibly because of their thick peptidoglycan cell wall. We also demonstrated that prolonged seed coating for 12 h could effectively enhance the colonization of C. pinensis, an endophytic bacterium, but not the rhizosphere colonizing C. rhizosphaerae. In the field only a small amount of inoculant was detected in the rhizosphere. This comparison demonstrates the importance of using the appropriate inoculation method for testing different types of bacteria for their plant growth-promotion potential.

Fosp9, a novel secreted protein, is essential for full virulence of Fusarium oxysporum f. sp. cubense on banana (Musa spp.)

The banana vascular wilt pathogen, Fusarium oxysporum f. sp. cubense, delivers a number of different secreted proteins into host plant tissues during infection. Until now, only a few of the secreted proteins from this fungus have been shown to be virulence effectors. Here, the product of fosp9, which is a gene from this pathogen, was found to be a novel virulence effector. The fosp9 gene encodes a hypothetical 185 amino acid protein which has a functional signal peptide, but contains no known motifs or domains. The fosp9 disruptants displayed a significant reduction in producing wilt symptoms on bananas, indicating that fosp9 is essential for the full virulence of this pathogen towards banana. These disruptants did not exhibit a change in either saprophytic growth or conidiation on potato dextrose agar medium, but their invasive growth in the rhizomes of banana was markedly compromised, suggesting a pivotal role for fosp9 in the colonization of banana rhizome tissues by this fungus. Live-cell imaging revealed that the Fosp9:GFP fusion protein accumulated in the apoplast of the plant cells. Moreover, transcriptome profiling revealed that a number of virulence-associated genes were differentially expressed in the fosp9 disruptant relative to the wild-type. Taken together, these findings suggest that Fosp9 is a genuine effector of F. oxysporum f. sp. cubense. IMPORTANCE Fusarium wilt of bananas (also known as Panama disease) caused by the fungus F. oxysporum f. sp. cubense is one of the most devastating banana diseases worldwide. The understanding of molecular mechanism of its pathogenicity is very limited until now. We demonstrated that the secreted protein Fosp9 from this fungus contributed to its virulence against banana hosts, and was essential for colonization of banana rhizome tissues by this fungus. Especially, Fosp9 contains no any known domains or motifs, and has no functionally characterized homologs, implying that it is a novel secreted effector involved in F. oxysporum f. sp. cubense- banana interactions. This work provides insight into molecular mechanisms of F. oxysporum f. sp. cubense pathogenicity, and the fosp9 gene characterized would facilitates us develop transgenic banana and plantain resistant to this disease by silencing of this effector gene through host-induced gene silencing or other strategies in future.

Tolerance of pesticides and antibiotics among beneficial soil microbes recovered from contaminated rhizosphere of edible crops

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Soil bacterial isolates were recovered from contaminated rhizosphere regions.

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Majority of bacterial isolatesshowed multifarious plant growth promoting (PGP) activities.

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Bacterial isolates exhibited a varied level of pesticide tolerance.

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Sensitivity/resistance pattern among isolates was variable

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Pesticides tolerance and antibiotic resistance among soil isolates were variably correlated

A total of 45 beneficial soil bacterial isolates (15 each of Pseudomonas, Azotobacter and phosphate solubilizing bacteria: PSB) recovered from polluted rhizosphere soils were morphologically and biochemically characterized. Bacterial isolates produced indole-3-acetic acid (IAA), phenolate siderophores; SA (salicylic acid) and 2, 3-dihydroxy benzoic acid (2, 3-DHBA), 1-amino cyclopropane 1-carboxylate (ACC) deaminase, solubilised insoluble phosphate (Pi), secreted exopolysaccharides (EPS) and produced ammonia and cyanogenic compound (HCN). Isolates were tested for their tolerance ability against 12 different agrochemicals (chemical pesticides) and 14 antibiotics. Among Pseudomonas, isolate PS1 showed maximum (2183 µg mL⁻¹) tolerance to all tested agrochemicals. Likewise, among all Azotobacter isolates (n = 15), AZ12 showed maximum (1766 µg mL⁻¹) while AZ7 had lowest (950 µg mL⁻¹) tolerance ability to all tested agrochemicals. Moreover, among phosphate solubilizing bacterial isolates, maximum (1970 µg mL⁻¹) and minimum (1308 µg mL⁻¹) tolerance to agrochemicals was represented by PSB8 and PSB13 isolates, respectively. The antibiotic sensitivity/resistance among isolates varied considerably. As an example, Pseudomonas spp. was susceptible to several antibiotics, and inhibition zone differed between 10 mm (polymyxin B) to 34 mm (nalidixic acid). Also, isolate PS2 showed resistance to erythromycin, ciprofloxacin, methicillin, novobiocin and penicillin. The resistance percentage to multiple antibiotics among Azotobacter isolates varied between 7 and 33%. Among PSB isolates, inhibition zone differed between 10 and 40 mm and maximum and minimum resistance percentage to multiple antibiotics was recorded as 47% and 20%, respectively. The persistence of pesticides in agricultural soil may contribute to an increase in multidrug resistance among soil microorganisms. In conclusion, plant growth promoting (PGP) substances releasing soil microorganisms comprising of inherent/intrinsic properties of pesticides tolerance and antibiotics resistance may provide an attractive, agronomically feasible, and long-term prospective alternative for the augmentation of edible crops. However, in future, more research is needed to uncover the molecular processes behind the development of pesticide tolerance and antibiotic resistance among soil microorganisms.

Pseudomonas mediated nutritional and growth promotional activities for sustainable food security

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Fluorescent and non-fluorescent species of Pseudomonas are important for plant growth promotion, phytopathogenic control and plant disease management.

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Pseudomonas belong to Pseudomonadaceae family (10 groups on the basis of rRNA-DNA hybridization) classified into 6-subgroups of rRNA gene homology and RFLP.

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Pseudomonas species produce antagonistic mechanism such as ISR and compounds like cell wall degradation enzymes, and antibiotics to maintain a mutualistic relationship with the associated plant.

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Pseudomonas sp. synthesize auxins having properties similar to phytohormones like IAA, which act as signaling molecules for regulating plant growth.

Numerous microbial communities show synergistic and antagonistic interactions among themselves, resulting in benefit and harm to either or both the associated members. The association holds accountability for nutrients recycling and energy drift, resulting in the availability of macronutrients unavailable and insoluble forms of rhizospheric nutrients, crucial for vital processes in plants, e.g., act as co-factors of various phyto-enzyme and redox mediators. Plant growth promoting rhizobacteria are known to enhance plant growth by increasing these macronutrients availability during their plant root colonization. In comparison to any other genera, Pseudomonas is the most favored bioinoculant due to its significant properties in both plant growth and phytopathogen control during its synergistic association with the host plant. These properties include siderophore production, phosphate solubilization, nitrogen fixation, phenazines, antibiotics, and induced systemic resistance carried out by various Pseudomonas species like Pseudomonas fluorescens, Pseudomonas putida, and Pseudomonas syringae. The association of Pseudomonas with crop plants procures several secretory and electron-based feedback mechanisms in order to regulate the plant growth and phytopathogen control activities through the secretion of several phytohormones (auxins, gibberellins, Indole-3-acetic acid), secondary metabolites (flavonoids) and enzymes (aminocyclopropane-1-carboxylate, phenylalanine ammonia-lyase). Ecologically significant applications of Pseudomonas in biocontrol and bioaugmentation are crucial for maintaining food security.

Lysinibacillus xylanilyticus Strain GIC41 as a Potential Plant Biostimulant

To identify Lysinibacillus strains with the potential to function as plant biostimulants, we screened 10 previously isolated Lysinibacillus strains from the rhizosphere and soil for their plant growth-promoting (PGP) effects. In vitro tests showed that all strains produced indole-3-acetic acid. In primary screening, the PGP effects of these strains were assessed on spinach seedlings grown on Jiffy-7 pellets; strains GIC31, GIC41, and GIC51 markedly promoted shoot growth. In secondary screening, the PGP efficacies of these three strains were examined using spinach seedlings grown in pots under controlled conditions. Only GIC41 exerted consistent and significant PGP effects; therefore, it was selected for subsequent experiments. The results of 6-week glasshouse experiments revealed that GIC41 markedly increased shoot dry weight by ca. 12–49% over that of the control. The impact of fertilization levels on the PGP efficacy of GIC41 was investigated using pot experiments. The application of a specific level of fertilizer was required for the induction of sufficient PGP effects by this strain. The phylogenetic ana­lysis based on the 16S rDNA sequence identified GIC41 as L. xylanilyticus. Collectively, these results show the potential of strain GIC41 to function as a plant biostimulant.

Bacillus cereus Improves Performance of Brazilian Green Dwarf Coconut Palms Seedlings With Reduced Chemical Fertilization

Coconut production in the Amazon requires the knowledge and development of sustainable technologies to alleviate the detrimental effects of inorganic chemical fertilizers and intensive farming practices. In this study, we investigated the effects of plant growth-promoting rhizobacteria (PGPR) isolated from coconut seedlings on nutrient use efficiency (NUE) and physiological mechanisms related to biomass accumulation of seedlings grown with reduced inorganic fertilizer levels. Of the 96 PGPR isolates tested on rice plants, the isolate Bacillus cereus (UFRABC40) was selected, as it resulted in the most significant gain in growth variables. In a commercial coconut tree nursery, we subjected seedlings to two treatments, both with seven replications: control 100% NPK chemical fertilizer (CF) and B. cereus + 50% NPK CF. The results indicated that the inoculation increased phytohormone levels [190% indole acetic acid (IAA), 31% gibberellic acid GA3, and 17% gibberellic acid GA4] and leaf gas exchange [48% by assimilation of CO2 (A), 35% stomatal conductance to water vapor (gs), 33% transpiration, and 57% instantaneous carboxylation efficiency] in leaves. Furthermore, growth parameters (shoot, root, and total dry weight, height, and diameter) and macro- and micronutrient levels (95% N, 44% P, 92% K, 103 Ca, 46% Fe, 84% B) were improved. Our results show the potential ability of strain Bacillus cereus UFRABC40 to promote the growth performance of coconut seedlings under decreased application of inorganic fertilizers. The application of microbial-based products in coconut seedling production systems improves plants' physiological performance and the efficiency of nutrient use.

Insights into the Interactions among Roots, Rhizosphere, and Rhizobacteria for Improving Plant Growth and Tolerance to Abiotic Stresses: A Review

Abiotic stresses, such as drought, salinity, heavy metals, variations in temperature, and ultraviolet (UV) radiation, are antagonistic to plant growth and development, resulting in an overall decrease in plant yield. These stresses have direct effects on the rhizosphere, thus severely affect the root growth, and thereby affecting the overall plant growth, health, and productivity. However, the growth-promoting rhizobacteria that colonize the rhizosphere/endorhizosphere protect the roots from the adverse effects of abiotic stress and facilitate plant growth by various direct and indirect mechanisms. In the rhizosphere, plants are constantly interacting with thousands of these microorganisms, yet it is not very clear when and how these complex root, rhizosphere, and rhizobacteria interactions occur under abiotic stresses. Therefore, the present review attempts to focus on root–rhizosphere and rhizobacterial interactions under stresses, how roots respond to these interactions, and the role of rhizobacteria under these stresses. Further, the review focuses on the underlying mechanisms employed by rhizobacteria for improving root architecture and plant tolerance to abiotic stresses.

Growth of Bacillus amyloliquefaciens as influence by Si nutrition

The aim of study was to determine the influence of soluble and solid forms of Si on the growth of B. amyloliquefaciens. The experiment was conducted at two regimes: under sterile conditions (without B. amyloliquefaciens) and infected conditions (with B. amyloliquefaciens). New formed silica gel, diatomite and monosilicic acid at 1 mM Si and 2 mM Si were used as source of Si. The concentration of monosilicic acid in the solution was measured on second and tenth days of experiment. The total carbon in the solution before and after centrifugation was determined on day 10 of the experiment. The experiment has demonstrated a significant positive effect (by 4.7-41.2%) on B. amyloliquefaciens growth in water system. The presence of B. amyloliquefaciens in Si-rich solution reduced the concentration of monosilicic acid in the solution up to 16.2%. About 13.5-30.7% of B. amyloliquefaciens can be attached to the Si-rich surface without formation of cell clusters. Si can be classified as a beneficial nutrient for B. amyloliquefaciens. The tested strain of Bacillus can form channels in silica gel. The presence of monosilicic acid resulted in the formation of an aligned positioning of cells in water-based solution. This study is the first to demonstrate the direct influence of active Si forms on bacteria growth. The research showed that monosilicic acid or Si-rich solid substances with high solubility on Si can be recommended to increase B. amyloliquefaciens growth in soil, water or reactors.

Biocontrol of Tomato Bacterial Wilt by Foliar Spray Application of a Novel Strain of Endophytic Bacillus sp

The aim of the present study was to identify a strain of endophytic Bacillus species that control tomato bacterial wilt by foliar spray application. Fifty heat-tolerant endophytic bacteria were isolated from the surface-sterilized foliar tissues of symptomless tomato plants that had been pre-inoculated with the pathogen Ralstonia pseudosolanacearum. In the primary screening, we assessed the suppressive effects of a shoot-dipping treatment with bacterial strains against bacterial wilt on tomato seedlings grown on peat pellets. Bacillus sp. strains G1S3 and G4L1 significantly suppressed the incidence of tomato bacterial wilt. In subsequent pot experiments, the biocontrol efficacy of foliar spray application was examined under glasshouse conditions. G4L1 displayed consistent and significant disease suppression, and, thus, was selected as a biocontrol candidate. Moreover, the pathogen population in the stem of G4L1-treated plants was markedly smaller than that in control plants. A quantitative real-time PCR analysis revealed that the foliar spraying of tomato plants with G4L1 up-regulated the expression of PR-1a and LoxD in stem and GluB in roots upon the pathogen inoculation, implying that the induction of salicylic acid-, jasmonic acid-, and ethylene-dependent defenses was involved in the protective effects of this strain. In the re-isolation experiment, G4L1 efficiently colonized foliar tissues for at least 4‍ ‍weeks after spray application. Collectively, the present results indicate that G4L1 is a promising biocontrol agent for tomato bacterial wilt. Furthermore, to the best of our knowledge, this is the first study to report the biocontrol of bacterial wilt by the foliar spraying with an endophytic Bacillus species.

Potential Use of Beneficial Microorganisms for Soil Amelioration, Phytopathogen Biocontrol, and Sustainable Crop Production in Smallholder Agroecosystems

Smallholder agroecosystems play a key role in the world's food security providing more than 50% of the food produced globally. These unique agroecosystems face a myriad of challenges and remain largely unsupported, yet they are thought to be a critical resource for feeding the projected increasing human population in the coming years. The new challenge to increase food production through agricultural intensification in shrinking per capita arable lands, dwindling world economies, and unpredictable climate change, has led to over-dependence on agrochemical inputs that are often costly and hazardous to both human and animal health and the environment. To ensure healthy crop production approaches, the search for alternative ecofriendly strategies that best fit to the smallholder systems have been proposed. The most common and widely accepted solution that has gained a lot of interest among researchers and smallholder farmers is the use of biological agents; mainly plant growth promoting microorganisms (PGPMs) that provide essential agroecosystem services within a holistic vision of enhancing farm productivity and environmental protection. PGPMs play critical roles in agroecological cycles fundamental for soil nutrient amelioration, crop nutrient improvement, plant tolerance to biotic and abiotic stresses, biocontrol of pests and diseases, and water uptake. This review explores different research strategies involving the use of beneficial microorganisms, within the unique context of smallholder agroecosystems, to promote sustainable maintenance of plant and soil health and enhance agroecosystem resilience against unpredictable climatic perturbations.

Bio-Mercury Remediation Suitability Index: A Novel Proposal That Compiles the PGPR Features of Bacterial Strains and Its Potential Use in Phytoremediation

Soil pollution from heavy metals, especially mercury, is an environmental problem for human health. Biological approaches offer interesting tools, which necessarily involve the selection of organisms capable of transforming the environment via bioremediation. To evaluate the potential use of microorganisms in phytorhizoremediation, bacterial strains were isolated from rhizospheric and bulk soil under conditions of chronic natural mercury, which were identified and characterized by studying the following: (i) their plant growth promoting rhizobacteria (PGPR) activities; and (ii) their maximum bactericide concentration of mercury. Information regarding auxin production, phosphate solubilization, siderophore synthesis and 1-aminocyclopropane-1-carboxylic acid deaminase (ACCd) capacity of the isolates was compiled in order to select the strains that fit potential biotechnological use. To achieve this objective, the present work proposes the Bio-Mercury Remediation Suitability Index (BMR-SI), which reflects the integral behavior of the strains for heavy metal polluted soil bioremediation. Only those strains that rigorously fulfilled all of the established criteria were selected for further assays.

Plant Growth Promotion Function of Bacillus sp. Strains Isolated from Salt-Pan Rhizosphere and Their Biocontrol Potential against Macrophomina phaseolina

In recent decades, intensive crop management has involved excessive use of pesticides or fertilizers, compromising environmental integrity and public health. Accordingly, there has been worldwide pressure to find an eco-friendly and safe strategy to ensure agricultural productivity. Among alternative approaches, Plant Growth-Promoting (PGP) rhizobacteria are receiving increasing attention as suitable biocontrol agents against agricultural pests. In the present study, 22 spore-forming bacteria were selected among a salt-pan rhizobacteria collection for their PGP traits and their antagonistic activity against the plant pathogen fungus Macrophomina phaseolina. Based on the higher antifungal activity, strain RHFS10, identified as Bacillus vallismortis, was further examined and cell-free supernatant assays, column purification, and tandem mass spectrometry were employed to purify and preliminarily identify the antifungal metabolites. Interestingly, the minimum inhibitory concentration assessed for the fractions active against M. phaseolina was 10 times lower and more stable than the one estimated for the commercial fungicide pentachloronitrobenzene. These results suggest the use of B. vallismortis strain RHFS10 as a potential plant growth-promoting rhizobacteria as an alternative to chemical pesticides to efficiently control the phytopathogenic fungus M. phaseolina.

Harvesting the complex pathways of antibiotic production and resistance of soil bacilli for optimizing plant microbiome

A sustainable future increasing depends on our capacity to utilize beneficial plant microbiomes to meet our growing needs. Plant microbiome symbiosis is a hallmark of the beneficial interactions between bacteria and their host. Specifically, colonization of plant roots by biocontrol agents and plant growth-promoting bacteria can play an important role in maintaining the optimal rhizosphere environment, supporting plant growth and promoting its fitness. Rhizosphere communities confer immunity against a wide range of foliar diseases by secreting antibiotics and activating plant defences. At the same time, the rhizosphere is a highly competitive niche, with multiple microbial species competing for space and resources, engaged in an arms race involving the production of a vast array of antibiotics and utilization of a variety of antibiotic resistance mechanisms. Therefore, elucidating the mechanisms that govern antibiotic production and resistance in the rhizosphere is of great significance for designing beneficial communities with enhanced biocontrol properties. In this review, we used Bacillus subtilis and B. amyloliquefaciens as models to investigate the genetics of antibiosis and the potential for its translation of into improved plant microbiome performance.

Bacterial Fertilizers Based on Rhizobium laguerreae and Bacillus halotolerans Enhance Cichorium endivia L. Phenolic Compound and Mineral Contents and Plant Development

Today there is an urgent need to find new ways to satisfy the current and growing food demand and to maintain crop protection and food safety. One of the most promising changes is the replacement of chemical fertilizers with biofertilizers, which include plant root-associated beneficial bacteria. This work describes and shows the use of B. halotolerans SCCPVE07 and R. laguerreae PEPV40 strains as efficient biofertilizers for escarole crops, horticultural species that are widely cultivated. An in silico genome study was performed where coding genes related to plant growth promoting (PGP) mechanisms or different enzymes implicated in the metabolism of phenolic compounds were identified. An efficient bacterial root colonization process was also analyzed through fluorescence microscopy. SCCPVE07 and PEPV40 promote plant development under normal conditions and saline stress. Moreover, inoculated escarole plants showed not only an increase in potassium, iron and magnesium content but also a significant improvement in protocatechuic acid, caffeic acid or kaempferol 3-O-glucuronide plant content. Our results show for the first time the beneficial effects in plant development and the food quality of escarole crops and highlight a potential and hopeful change in the current agricultural system even under saline stress, one of the major non-biological stresses.

Isolation, Biochemical and Genomic Characterization of Glyphosate Tolerant Bacteria to Perform Microbe-Assisted Phytoremediation

The large-scale use of the herbicide glyphosate leads to growing ecotoxicological and human health concerns. Microbe-assisted phytoremediation arises as a good option to remove, contain, or degrade glyphosate from soils and waterbodies, and thus avoid further spreading to non-target areas. To achieve this, availability of plant-colonizing, glyphosate-tolerant and -degrading strains is required and at the same time, it must be linked to plant-microorganism interaction studies focusing on a substantive ability to colonize the roots and degrade or transform the herbicide. In this work, we isolated bacteria from a chronically glyphosate-exposed site in Argentina, evaluated their glyphosate tolerance using the minimum inhibitory concentration assay, their in vitro degradation potential, their plant growth-promotion traits, and performed whole genome sequencing to gain insight into the application of a phytoremediation strategy to remediate glyphosate contaminated agronomic soils. Twenty-four soil and root-associated bacterial strains were isolated. Sixteen could grow using glyphosate as the sole source of phosphorous. As shown in MIC assay, some strains tolerated up to 10000 mg kg^–1 of glyphosate. Most of them also demonstrated a diverse spectrum of in vitro plant growth-promotion traits, confirmed in their genome sequences. Two representative isolates were studied for their root colonization. An isolate of Ochrobactrum haematophilum exhibited different colonization patterns in the rhizoplane compared to an isolate of Rhizobium sp. Both strains were able to metabolize almost 50% of the original glyphosate concentration of 50 mg l^–1 in 9 days. In a microcosms experiment with Lotus corniculatus L, O. haematophilum performed better than Rhizobium, with 97% of glyphosate transformed after 20 days. The results suggest that L. corniculatus in combination with to O. haematophilum can be adopted for phytoremediation of glyphosate on agricultural soils. An effective strategy is presented of linking the experimental data from the isolation of tolerant bacteria with performing plant-bacteria interaction tests to demonstrate positive effects on the removal of glyphosate from soils.

Streptomyces sp. strain TOR3209: a rhizosphere bacterium promoting growth of tomato by affecting the rhizosphere microbial community

Aiming at revealing the possible mechanism of its growth promoting effect on tomato, the correlations among Streptomyces sp. TOR3209 inoculation, rhizobacteriome, and tomato growth/production traits were investigated in this study. By analyses of Illumina sequencing and plate coating, differences in rhizosphere microbial communities were found in different growth stages and distinct inoculation treatments. The plant biomass/fruit yields and relative abundances of families Flavobacteriaceae, Sphingobacteriaceae, Polyangiaceae and Enterobacteriaceae in treatments T (tomato inoculated with TOR3209) and TF (tomato inoculated with TOR3209 + organic fertilizer) were higher than that in the controls (CK and CK+ organic fertilizer), respectively. The analysis of Metastats and LEfSe revealed that the genera Flavobacterium and Sorangium in seedling stage, Klebsiella in flowering stage, Collimonas in early fruit setting stage, and genera Micrococcaceae, Pontibacte and Adhaeribacter in late fruit setting stage were the most representative rhizobacteria that positively responded to TOR3209 inoculation. By cultivation method, five bacterial strains positively correlated to TOR3209 inoculation were isolated from rhizosphere and root endosphere, which were identified as tomato growth promoters affiliated to Enterobacter sp., Arthrobacter sp., Bacillus subtilis, Rhizobium sp. and Bacillus velezensis. In pot experiment, TOR3209 and B. velezensis WSW007 showed joint promotion to tomato production, while the abundance of inoculated TOR3209 was dramatically decreased in rhizosphere along the growth of tomato. Conclusively, TOR3209 might promote the tomato production via changing of microbial community in rhizosphere. These findings provide a better understanding of the interactions among PGPR in plant promotion.

Complementary Dynamics of Banana Root Colonization by the Plant Growth-Promoting Rhizobacteria Bacillus amyloliquefaciens Bs006 and Pseudomonas palleroniana Ps006 at Spatial and Temporal Scales

Banana (Musa acuminata) growth for commercial purposes requires high amounts of chemical fertilizers, generating high costs and deleterious effects on the environment. In a previous study, we demonstrated that two plant growth-promoting rhizobacteria (PGPR), Bacillus amyloliquefaciens Bs006 and Pseudomonas palleroniana Ps006, isolated in Colombia, could partially replace chemical fertilizers for banana seedling growth. In a second work, the effects of the two inoculants on banana transcripts were found to occur at different times, earlier for Bs006 and later for Ps006. This leads to the hypothesis that the two rhizobacteria have different colonization dynamics. Accordingly, the aim of this work was to analyze the dynamics of root colonization of the two PGPR, Bs006 and Ps006, on banana growth over a time frame of 30 days. We used fluorescence in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM), followed by three-dimensional reconstruction and quantitative image analysis. Bacillus amyloliquefaciens Bs006 abundantly colonized banana roots earlier (from 1 to 48 h), ectophytically on the rhizoplane, and then decreased. Pseudomonas palleroniana Ps006 was initially scarce, but after 96 h it increased dramatically and became clearly endophytic. Here we identify and discuss the potential genetic factors responsible for this complementary behavior. This information is crucial for optimizing the formulation of an effective biofertilizer for banana and its inoculation strategy.

Framework for Quantification of the Dynamics of Root Colonization by Pseudomonas fluorescens Isolate SBW25

Colonization of the root surface, or rhizoplane, is one of the first steps for soil-borne bacteria to become established in the plant microbiome. However, the relative contributions of processes, such as bacterial attachment and proliferation is not well characterized, and this limits our ability to comprehend the complex dynamics of microbial communities in the rhizosphere. The work presented here addresses this knowledge gap. A model system was developed to acquire quantitative data on the colonization process of lettuce (Lactuca sativa L. cultivar. All Year Round) roots by Pseudomonas fluorescens isolate SBW25. A theoretical framework is proposed to calculate attachment rate and quantify the relative contribution of bacterial attachment to colonization. This allows the assessment of attachment rates on the root surface beyond the short time period during which it can be quantified experimentally. All techniques proposed are generic and similar analyses could be applied to study various combinations of plants and bacteria, or to assess competition between species. In the future this could allow for selection of microbial traits that improve early colonization and maintenance of targeted isolates in cropping systems, with potential applications for the development of biological fertilizers.

Effect of Chemical Fertilization on the Impacts of Plant Growth-Promoting Rhizobacteria in Maize Crops

The use of chemical fertilizers strongly promotes productivity in agricultural crops; therefore, large amounts of chemical fertilizers have been used. The use of plant growth-promoting bacteria may be a strategy to reduce the use of chemical fertilizers; however, little is known about the effect of chemical fertilization on the performance of these bacteria through plant-microbe interactions. The present study aimed to verify the performance of Bacillus subtilis, Azospirillum brasilense, B. pumilus, B. amyloliquefaciens, Herbaspirillum seropedicae, Gluconacetobacter diazotrophicus, and the mixtures A. brasilense + B. subtilis, B. pumilus + B. amyloliquefaciens, and H. seropedicae + G. diazotrophicus on parameters such as nitrogen and phosphorus extraction from soil, the concentrations of these nutrients in maize plants, and plant growth in both fertilized and unfertilized soil. The results showed that H. seropedica increased the nitrogen content by 6.6 g kg^-1 in leaves and 2.2 g kg^-1 in the root when comparing the unfertilized with the fertilized condition. G. diazotrophicus increased the nitrogen content by 3.7 g kg^-1 in leaves and 2.4 g kg^-1 in the root. B. pumilus increased the phosphorous content by 1.7 g kg^-1 in leaves, and B. amyloliquefaciens increased the phosphorous content by 0.61 g kg^-1. The present study showed that even though the bacteria presented good performance related to plant growth under fertilized conditions, H. seropedicae, G. diazotrophicus, B. pumilus, and B. amyloliquefaciens could be used in the maize crop with a reduced chemical fertilization dose.

Actinomycete Strains Isolated from Saline Soils: Plant-Growth-Promoting Traits and Inoculation Effects on Solanum lycopersicum

Excessive use of chemical products in agriculture is causing significant environmental pollution and the loss of lands and fertility of agricultural soils. Plant-growth-promoting bacteria are a valid alternative strategy for sustainable agriculture. The aim of this study was to select actinomycete strains based on their plant-growth-promoting traits and to investigate their root association abilities and biostimulant effects on Solanum lycopersicum. The strains were investigated for their phosphate solubilization ability, production of indole-3-acetic acid, hydrocyanic acid, and ammonia, and several enzymatic activities. Bacteria–plant-root associations were studied by scanning electron microscopy. A greenhouse experiment was carried out to assess inoculation effects. Of sixty isolates, fourteen strains showed significant plant-growth-promoting traits. All fourteen strains solubilized phosphate, produced ammonia, and showed several enzymatic activities at different rates. The production of indole-3-acetic acid was shown by nine strains, while hydrocyanic acid production was observed in eleven of them. Scanning electron microscopy revealed that strains have good in vitro plant root association and colonization abilities. In planta inoculation by actinomycete strains positively influenced plant growth parameters. The best results were shown by seven actinomycete strains, suggesting their possible utilization as biofertilizer agents for sustainable agriculture.

Banana (Musa acuminata) transcriptome profiling in response to rhizobacteria: Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006

Background

Banana is one of the most important crops in tropical and sub-tropical regions. To meet the demands of international markets, banana plantations require high amounts of chemical fertilizers which translate into high farming costs and are hazardous to the environment when used excessively. Beneficial free-living soil bacteria that colonize the rhizosphere are known as plant growth-promoting rhizobacteria (PGPR). PGPR affect plant growth in direct or indirect ways and hold great promise for sustainable agriculture.

Results

PGPR of the genera Bacillus and Pseudomonas in banana cv. Williams were evaluated. These plants were produced through in vitro culture and inoculated individually with two rhizobacteria, Bacillus amyloliquefaciens strain Bs006 and Pseudomonas fluorescens strain Ps006. Control plants without microbial inoculum were also evaluated. These plants were kept in a controlled climate growth room with conditions required to favor plant-microorganism interactions. These interactions were evaluated at 1-, 48- and 96-h using transcriptome sequencing after inoculation to establish differentially expressed genes (DEGs) in plants elicited by the interaction with the two rhizobacteria. Additionally, droplet digital PCR was performed at 1, 48, 96 h, and also at 15 and 30 days to validate the expression patterns of selected DEGs. The banana cv. Williams transcriptome reported differential expression in a large number of genes of which 22 were experimentally validated. Genes validated experimentally correspond to growth promotion and regulation of specific functions (flowering, photosynthesis, glucose catabolism and root growth) as well as plant defense genes. This study focused on the analysis of 18 genes involved in growth promotion, defense and response to biotic or abiotic stress.

Conclusions

Differences in banana gene expression profiles in response to the rhizobacteria evaluated here (Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006) are influenced by separate bacterial colonization processes and levels that stimulate distinct groups of genes at various points in time.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5763-5) contains supplementary material, which is available to authorized users.

Bioactive Products From Plant-Endophytic Gram-Positive Bacteria

Endophytes constitute plant-colonizing microorganisms in a mutualistic symbiosis relationship. They are found in most ecosystems reducing plant crops' biotic and abiotic stressors by stimulating immune responses, excluding plant pathogens by niche competition, and participating in antioxidant activities and phenylpropanoid metabolism, whose activation produces plant defense, structural support, and survival molecules. In fact, metabolomic studies have demonstrated that endophyte genes associated to specific metabolites are involved in plant growth promotion (PGP) by stimulating plant hormones production such as auxins and gibberellins or as plant protective agents against microbial pathogens, cancer, and insect pests, but eco-friendly and eco-safe. A number of metabolites of Gram-positive endophytes isolated from agriculture, forest, mangrove, and medicinal plants, mainly related to the Firmicutes phyla, possess distinctive biocontrol and plant growth-promoting activities. In general, Actinobacteria and Bacillus endophytes produce aromatic compounds, lipopeptides, plant hormones, polysaccharides, and several enzymes linked to phenylpropanoid metabolism, thus representing high potential for PGP and crop management strategies. Furthermore, Actinobacteria have been shown to produce metabolites with antimicrobial and antitumor activities, useful in agriculture, medicine, and veterinary areas. The great endophytes diversity, their metabolites production, and their adaptation to stress conditions make them a suitable and unlimited source of novel metabolites, whose application could reduce agrochemicals usage in food and drugs production.