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While horticulture tools and methods have been extensively developed to improve the management of crops, systems to harness the rhizosphere microbiome to benefit plant crops are still in development. Plants and microbes have been coevolving for several millennia, conferring fitness advantages that expand the plant’s own genetic potential. These beneficial associations allow the plants to cope with abiotic stresses such as nutrient deficiency across a wide range of soils and growing conditions. Plants achieve these benefits by selectively recruiting microbes using root exudates, positively impacting their nutrition, health and overall productivity. Advanced knowledge of the interplay between root exudates and microbiome alteration in response to plant nutrient status, and the underlying mechanisms there of, will allow the development of technologies to increase crop yield. This review summarizes current knowledge and perspectives on plant–microbial interactions for resource acquisition and discusses promising advances for manipulating rhizosphere microbiomes and root exudation.

Rhizobacterial communities can contribute to plant trait expression and performance, including plant tolerance against abiotic stresses such as drought. The conditioning of microbial communities related to disease resistance over generations has been shown to develop suppressive soils which aid in plant defense responses. Here, we applied this concept for the development of drought resistant soils. We hypothesized that soils conditioned under severe drought stress and tomato cultivation over two generations, will allow for plant selection of rhizobacterial communities that provide plants with improved drought resistant traits. Surprisingly, the plants treated with a drought-conditioned microbial inoculant showed significantly decreased plant biomass in two generations of growth. Microbial community composition was significantly different between the inoculated and control soils within each generation (i.e., microbial history effect) and for the inoculated soils between generations (i.e., conditioning effect). These findings indicate a substantial effect of conditioning soils on the abiotic stress response and microbial recruitment of tomato plants undergoing drought stress.

Insects are known plant pests, and some of them such as Trichoplusia ni feed on a variety of crops. In this study, Trichoplusia ni was fed distinct diets of leaves of Arabidopsis thaliana or Solanum lycopersicum as well as an artificial diet. After four generations, the microbial composition of the insect gut was evaluated to determine if the diet influenced the structure and function of the microbial communities. The population fed with A. thaliana had higher proportions of Shinella, Terribacillus and Propionibacterium, and these genera are known to have tolerance to glucosinolate activity, which is produced by A. thaliana to deter insects. The population fed with S. lycopersicum expressed increased relative abundances of the Agrobacterium and Rhizobium genera. These microbial members can degrade alkaloids, which are produced by S. lycopersicum. All five of these genera were also present in the respective leaves of either A. thaliana or S. lycopersicum, suggesting that these microbes are acquired by the insects from the diet itself. This study describes a potential mechanism used by generalist insects to become habituated to their available diet based on acquisition of phytochemical degrading gut bacteria.

Soil microbiome disruption methods are regularly used to reduce populations of microbial pathogens, often resulting in increased crop growth. However, little is known about the effect of soil microbiome disruption on non-pathogenic members of the soil microbiome. Here, we applied soil microbiome disruption in the form of moist-heat sterilization (autoclaving) to reduce populations of naturally occurring soil microbiota. The disruption was applied to analyze bacterial community rearrangement mediated by four crops (corn, beet, lettuce, and tomato) grown in three historically distinct agroecosystem soils (conventional, organic, and diseased). Applying the soil disruption enhanced plant influence on rhizosphere bacterial colonization, and significantly different bacterial communities were detected between the tested crops. Furthermore, bacterial genera showed significant abundance increases in ways both unique-to and shared-by each tested crop. As an example, corn uniquely promoted abundances of Pseudomonas and Sporocytophaga, regardless of the disrupted soil in which it was grown. Whereas the promotion of Bosea, Dyadobacter and Luteoliobacter was shared by all four crops when grown in disrupted soils. In summary, soil disruption followed by crop introduction amplified the plant colonization of potential beneficial bacterial genera in the rhizosphere.

Aims This study builds upon the premise that roots culture distinct bacteria at specific stages of plant growth to benefit of specific microbial services needed at that particular growth stage. Accordingly, we hypothesized that the co-inoculation of beneficial microbes with distinct properties at specific stages of plant development would enhance plant performance. Methods and results The chosen microbes were Bacillus pumilus, Bacillus amyloliquefaciens, Bacillus mojavensis and Pseudomonas putida. These microbes were selected based on their specific services ranging from nutrient solubilization, root growth promotion and disease resistance, and were applied to the roots of tomato plants at specific time points when those services were needed the most by the plant. Laboratory and greenhouse studies were conducted to evaluate the effects of co-inoculation at specific stages of development compared to single microbial applications. Conclusion In general, the combination of three microbes gave the highest biomass and yield without the presence of disease. Applications of three microbes showed the highest root/shoot ratio, and applications of four microbes the lowest ratio. Pseudomonas putida significantly increased fruit macronutrient and micronutrient contents. Significance and impact of the study Our studies suggest that co-inoculation of three or four microbes is a good strategy for healthy crop production.

Root-knot nematodes (RKN) such as Meloidogyne spp. are among the most detrimental pests in agriculture affecting several crops. New methodologies to manage RKN are needed such as efficient discovery of nematophagous microbes. In this study, we developed an in vitro high-throughput method relying on the free-living nematode Caenorhabditis elegans and the infection of those nematodes with a soil slurry containing a microbiome likely to house nematophagous microbes. Nematodes were monitored for presence of infection and sub-cultured repeatedly for the purpose of isolating pure cultures of the microbe responsible for conferring the nematicidal activity. Once soil microbes were confirmed to be antagonistic to C. elegans, they were tested for pathogenicity against Meloidogyne chitwoodi. Using this methodology, the fungal isolate Mortierella globalpina was confirmed to be pathogenic in vitro against M. chitwoodi by nematode trapping via hyphal adhesion to the cuticle layer, penetration of the cuticle layer, and subsequently digestion of its cellular contents. M. globalpina was also observed to reduce disease symptomology of RKNs in vivo via significant reduction of root-galls on tomato (Solanum lycopersicum var. Rutgers).

Soil microbiome disruption methods are regularly used to reduce populations of microbial pathogens, which often results in increase crop growth. However, little is known about the effect of soil microbiome disruption on non-pathogenic members within the soil microbiome. Here, we applied soil microbiome disruption, in the form of moist-heat sterilization (autoclaving) to reduce populations of naturally occurring soil microbiota. The disruption was applied to analyze bacterial community rearrangement mediated by four crops (corn, beet, lettuce, and tomato) grown in three historically distinct agroecosystem soils (conventional, organic, and diseased). Applying the soil disruption enhanced plant influence on bacterial colonization, and significantly different bacterial communities were detected between the tested crops. Furthermore, bacterial genera showed significant abundance increases both unique-to and shared-by each tested crop. As an example, corn uniquely promoted abundances of Pseudomonas and Sporocytophaga, regardless of the disrupted soil in which it was grown. Whereas the promotion of Bosea, Dyadobacter and Luteoliobacter was shared by all crops grown in all disrupted soils. In summary, soil disruption followed by crop introduction amplified plant-mediated selection of plant benefiting bacterial genera.

Plant root exudation has long been recognized as a vital communication system between plants and microbial communities populating the rhizosphere. Due to the high complexity of the collection process and analysis, a variety of techniques have been developed to mimic natural exudation conditions. In addition, significant progress improving existing techniques and developing new methodologies of root exudate collection and analysis have been made. However, optimal standard methods that compare closely with environmental soil conditions are not yet available. In this review, we provide an overview of all those topics and provide suggestions for improvement.

Plant root exudation has long been recognized as a vital communication system between plants and microbial communities populating the rhizosphere. Due to the high complexity of the collection process and analysis, a variety of techniques have been developed to mimic natural exudation conditions. In addition, significant progress improving existing techniques and developing new methodologies of root exudate collection and analysis have been made. However, optimal standard methods that compare closely with environmental soil conditions are not yet available. In this review, we provide an overview of all those topics and provide suggestions for improvement.

Although interactions between plants and microbes at the plant-soil interface are known to be important for plant nutrient acquisition, relatively little is known about how root exudates contribute to nutrient exchange over the course of plant development. In this study, root exudates from slow- and fast-growing stages of Arabidopsis thaliana plants were collected, chemically analysed and then applied to a sandy nutrient-depleted soil. We then tracked the impacts of these exudates on soil bacterial communities, soil nutrients (ammonium, nitrate, available phosphorus and potassium) and plant growth. Both pools of exudates shifted bacterial community structure. GeoChip analyses revealed increases in the functional gene potential of both exudate-treated soils, with similar responses observed for slow-growing and fast-growing plant exudate treatments. The fast-growing stage root exudates induced higher nutrient mineralization and enhanced plant growth as compared to treatments with slow-growing stage exudates and the control. These results suggest that plants may adjust their exudation patterns over the course of their different growth phases to help tailor microbial recruitment to meet increased nutrient demands during periods demanding faster growth.

The role of root exudates has long been recognized for its potential to improve nutrient use efficiency in cropping systems. However, studies addressing the variability of root exudates involved in phosphorus solubilization across plant developmental stages remain scarce. Here, we grew Arabidopsis thaliana seedlings in sterile liquid culture with a low, medium, or high concentration of phosphate and measured the composition of the root exudate at seedling, vegetative, and bolting stages. The exudates changed in response to the incremental addition of phosphorus, starting from the vegetative stage. Specific metabolites decreased in relation to phosphate concentration supplementation at specific stages of development. Some of those metabolites were tested for their phosphate solubilizing activity, and 3-hydroxypropionic acid, malic acid, and nicotinic acid were able to solubilize calcium phosphate from both solid and liquid media. In summary, our data suggest that plants can release distinct compounds to deal with phosphorus deficiency needs influenced by the phosphorus nutritional status at varying developmental stages.

Summary Plants can re‐programme their transcriptome, proteome and metabolome to deal with environmental and biotic stress. It has been shown that the rhizosphere microbiome has influence on the plant metabolome and on herbivore behaviour. In the present study, Trichoderma gamsii was isolated from Arabidopsis thaliana rhizosphere soil. The inoculation of roots of Arabidopsis thaliana with T. gamsii significantly inhibited the feeding behaviour of Trichoplusia ni and affected the metabolome as well as the content of phytohormones in Arabidopsis leaves. T. gamsii‐treated plant leaves had higher levels of amino acids and lower concentrations of sugars. In addition, T. gamsii‐treated plant leaves had more abscisic acid (ABA) and lower levels of salicylic acid (SA) and indole‐3‐acetic acid (IAA) in comparison with the untreated plants. Furthermore, the inoculation with T. gamsii on different signalling mutants showed that the induction of defences were SA‐dependent. These findings indicate that T. gamsii has potential as a new type of biocontrol agent to promote plant repellence to insect attacks.

Phosphorous (P) fertilization is critical to enhance plant P uptake and proper growth. Soil microorganisms play a key role in P cycle and mediating P availability to plants. However, it is presently unknown if its application may have detrimental effects on the soil bacterial community. Blueberries are sensitive to fertilization hinting to close relationships with beneficial microbes related to soil nutrition. Our study explored the effect of P fertilization amendments on soil bacterial community composition in two varieties of commercial blueberry (Vaccinium sp. var. “Misty” and “Biloxi”). Shifts in microbial community composition and diversity were found in response to P amendment. The rhizosphere microbiome was influenced by P level and differentiated based on low P (0 and 50 kg/ha) and high P (101 and 192 kg/ha) rates. Additionally, predictive microbial acid phosphatase activity decreased with increasing levels of decomposition and solubility of mineral P. Thus, our results suggest that P fertilization decreases the ability of P–solubilizing microbes to naturally provide P to the plant.

Some rhizosphere microbes, such as plant growth-promoting rhizobacteria (PGPR), can alleviate plant drought stress and improve water use efficiency and productivity under drought conditions. The aims of this study are: 1) isolation and characterization of PGPRs from the rhizosphere of Arabidopsis plants that could improve drought tolerance of Arabidopsis and maize; 2) studying the potential mechanisms of improved plant drought tolerance by the isolated bacteria. In this study, bacteria isolates were isolated from the rhizosphere of Arabidopsis plants subjected to water limitation. Subsequently, the isolates were cultured and screened for their ability to improve drought tolerance of Arabidopsis. Potential mechanisms of improved plant drought tolerance by these bacteria including bacterial exopolysaccharide and 1-aminocyclopropane-1-carboxylic acid deaminase production, plant root system architecture modification, and plant physiological responses were also explored. Two bacterial isolates that conferred the greatest drought tolerance to Arabidopsis were further characterized. Both bacteria exhibit 1-aminocyclopropane-1-carboxylic acid deaminase activity, which can promote drought tolerance by decreasing plant ethylene levels. In vitro study showed that both Mitsuaria sp. ADR17 and Burkholderia sp. ADR10 altered the root structure system of Arabidopsis. Moreover, inoculation of Zea mays L. with either strain reduced evapotranspiration (i.e., soil water loss), and changed the plant proline and malondialdehyde levels, antioxidant enzymes activity, and phytohormone contents under drought stress. These results indicate that both strains interact with plants in ways that allow them to alter root system architecture, plant physiological responses and phytohormone levels under drought conditions to alleviate stress and improve plant survival. The results also indicated that each individual isolate has a separate pleiotropic effect.

The underground root-soil-microbe interactions are extremely complex, but vitally important for aboveground plant growth, health and fitness. The pressure to reduce our reliance on agrochemicals, and sustainable efforts to develop agriculture makes rhizosphere interactions' research a hotspot. Recent advances provide new insights about the signals, pathways, functions and mechanisms of these interactions. In this review, we provide an overview about recent progress in rhizosphere interaction networks in crops. We also discuss a holistic view of the root-soil-rhizomicrobiome interactions achieved through the advances of omics and bioinformatics technologies, and the potential strategies to manage the complex rhizosphere interactions for enhancing crop production.

Pratylenchus neglectus and Meloidogyne chitwoodi are the main plant-parasitic nematodes in potato crops of the San Luis Valley, Colorado. Bacterial microbiome (16S rRNA copies per gram of soil) and nematode communities (nematodes per 200 g of soil) from five different potato farms were analyzed to determine negative and positive correlations between any bacterial genus and P. neglectus and M. chitwoodi. Farms showed differences in bacterial communities, percentage of bacterivorous and fungivorous nematodes, and numbers of P. neglectus and M. chitwoodi. The farm with the lowest population of P. neglectus and M. chitwoodi had higher abundances of the bacterial genera Bacillus spp., Arthrobacter spp., and Lysobacter spp., and the soil nematode community was composed of more than 30% of fungivorous nematodes. In contrast, the farm with higher numbers of P. neglectus and M. chitwoodi had a lower abundance of the abovementioned bacterial genera, higher abundance of Burkholderia spp., and less than 25% of fungivorous nematodes. The α-Proteobacteria Rhodoplanes, Phenylobacterium, and Kaistobacter positively correlated with M. chitwoodi, and the Bacteroidia and γ-Proteobacteria positively correlated with P. neglectus. Our results, based largely on co-occurrence analyses, suggest that the abundance of Bacillus spp., Arthrobacter spp., and Lysobacter spp. in Colorado potato soils is negatively correlated with P. neglectus and M. chitwoodi abundance. Further studies will isolate and identify bacterial strains of these genera, and evaluate their nematode-antagonistic activity.

There is evidence that shows that phosphorus (P) fertilization has a moderate effect on the rhizosphere microbial composition of cultivated crops. But how this effect is manifested on wild species of the same crop is not clear. This study compares the impact of phosphorus fertilization with rhizosphere bacterial community composition and its predicted functions, related to P-cycling genes, in both cultivated and non-cultivated potato (Solanum sp.) plants. It was found that the biomass of non-cultivated potatoes was more responsive to P fertilization as compared with cultivated plants. Differences in general bacterial community composition patterns under increasing P amendments were subtle for both potato groups. However, potato genotype significantly influenced community composition with several bacterial families being more abundant in the cultivated plants. In addition, the predicted phosphatases had lower abundances in modern cultivars compared with non-cultivated potatoes. In summary, despite higher accumulation of differentially abundant bacteria in the rhizosphere of cultivated plants, the responsiveness of these plants to increase P levels was lower than in non-cultivated plants.

Extracts of Mirabilis jalapa (Nyctaginaceae), containing a ribosome inactivating protein (RIP) called Mirabilis antiviral protein (MAP), were tested against infection by potato virus X, potato virus Y, potato leaf roll virus, and potato spindle tuber viroid. Root extracts of M. jalapa sprayed on test plants 24 h before virus or viroid inoculation inhibited infection by almost 100%, as corroborated by infectivity assays and the nucleic acid spot hybridization test. Antiviral activity of MAP extracts was observed against mechanically transmitted viruses but not against aphid-transmitted viruses. Purified MAP showed the same antiviral effect as the crude extracts.

Klebsiella pneumoniae was isolated from infected pupae of Galleria mellonella and Pseudomonas aeruginosa was isolated from the entomopathogenic nematode Heterorhabditis bacteriophora hosted within the pupae of G. mellonella. Insect consumption and surface application of P. aeruginosa resulted in 83.33% and 81.66% mortality of Trichoplusia ni larvae, respectively. In contrast, 50% mortality was shown when T. ni larvae were fed with K. pneumoniae, and no larvae were killed when applying the bacterium to the larval cuticle. This report shows that two opportunistic human pathogens found in the insect-nematode ecosystem could kill insect pests.

Organic farming is frequently touted as being beneficial to soil health by increasing microbial community diversity; however, contradictory results exist in the literature. In this study, we compared several organic and conventional potato farms in Colorado for differences in soil nutrients and microbial communities using 454 pyrosequencing of the 18S ribosomal RNA gene. Organic farms showed a slightly higher diversity and evenness within the microbial community compared with conventional farms. No difference in the number of observed or estimated total operational taxonomic units (OTUs) was observed between management strategies. However, the relative abundance of 16 OTUs (3% genetic distance) differed between the organic and conventional farms, with seven increasing and nine decreasing in organic farms. A variety of known potato fungal pathogens (e.g., Alternaria spp., Ulocladium spp., and Pythium ultimum) were detected in the soil, including three different OTUs (3% genetic distance) with a high homology to the early blight pathogen Alternaria solani. Relative abundance for Alternaria spp. was higher in conventional farms (relative abundance 30.15 versus 7.8%), whereas the relative abundance for P. ultimum was higher in organic farms (relative abundance 0.25 versus 0.05%). Quantitative polymerase chain reaction, using primers specific for A. solani, Phoma foveata, and Pythium ultimum, yielded similar results to the pyrosequencing, validating the use of pyrosequencing data for the quantification of OTU relative abundances.

The composition and function of microbial communities in the rhizosphere of crops have been linked to edaphic factors and root exudate composition. We examined the effect of N fertilizer (urea) rate on maize root exudation, the associated rhizosphere microbial community, and nitrogen-use-efficiency. Increasing N rate had a significant effect on root exudate quantity and composition. Specifically, the total abundance of sugars, sugar alcohols, and phenolics was positively correlated with N rate (p 0.05). However, on a total abundance basis (gene copies g−1 soil FW) all N-cycle genes increased significantly with increasing N rate (p

Although it is well known that diet is one of the major modulators of the gut microbiome, how the major components of diet shape the gut microbial community is not well understood. Here, we developed a simple system that allows the investigation of the impact of given compounds as supplements of the diet on the termite gut microbiome. The 16S rRNA pyrosequencing analysis revealed that feeding termites different blends of sugars and amino acids did not majorly impact gut community composition; however, ingestion of blends of secondary metabolites caused shifts in gut bacterial community composition. The supplementation of sugars and amino acids reduced the richness significantly, and sugars alone increased the evenness of the gut bacterial community significantly. Secondary metabolites created the most dramatic effects on the microbial community, potentially overriding the effect of other types of compounds. Furthermore, some microbial groups were stimulated specifically by particular groups of compounds. For instance, termites fed with secondary metabolites contained more Firmicutes and Spirochaetes compared to the other treatments. In conclusion, our results suggest that the termite (Reticulitermes flavipes) can be used as a simple and effective system to test the effects of particular chemical compounds in modulating the gut microbiome.

The unspecified components of plant-microbe and plant-microbiome associations in the rhizosphere are complex, but recent research is simplifying our understanding of these relationships. We propose that the strong association between hosts, symbionts, and pathogens could be simplified by the concept of soil memory, which explains how a plant could promote their fecundity and protect their offspring through tightly associated relationships with the soil. Although there are many questions surrounding the mechanisms of this phenomenon, recent research has exposed evidence of its existence. Along with evidence from observations and mechanisms related to soil memory, we report means to utilize our understanding as sustainable protection for agricultural crops and propose future research questions.

Plant growth-promoting rhizobacteria (PGPR) have garnered interest in agriculture due to their ability to influence the growth and production of host plants. ATP-binding cassette (ABC) transporters play important roles in plant-microbe interactions by modulating plant root exudation. The present study aimed to provide a more precise understanding of the mechanism and specificity of the interaction between PGPR and host plants. In the present study, the effects of interactions between a PGPR strain, Bacillus cereus AR156, and Arabidopsis thaliana wild type (Col-0) or its ABC transporter mutants on plant growth have been studied. B. cereus AR156 promoted the shoot growth of Col-0 and Atabcg30 but repressed the growth of Atabcc5. Bacterial volatiles and secretion promoted the shoot growth of Col-0 and Atabcg30 but had no effect on Atabcc5. We also found that root exudates of Col-0 induced the expression of B. cereus AR156 genes related to siderophore and chitinase production; while root exudates of Atabcc5 inhibited the expression level of those genes. Further analysis of root exudates revealed that amino acids, organic acids, and sugars were significantly less abundant in Atabcc5 when compared to Col-0. Our findings highlight that both host plant and PGPR play active roles in the outcome of the plant-microbe interaction.

Soil microbes live in close association with plants and are crucial for plant health and fitness. Recent literature revealed that specific microbes were cultured at distinct developmental stages of Arabidopsis. It is not clear how fast the roots, depending on their developmental stage, can alter the root-associated microbiome. In this study, Arabidopsis, grown under sterile conditions at precisely distinct developmental stages were supplied with a soil microbial slurry. Within four days, roots selected specific microorganisms depending on plant development, and Proteobacteria among other bacterial groups were found to colonize the roots irrespective of developmental stage. Moreover, exposure to a microbiome resulted in modulation of phytohormone levels at different stages of Arabidopsis.

Jasmonic acid (JA) is an essential hormone in plant development and defense responses in Arabidopsis thaliana. Exogenous treatment with JA has recently been shown to alter root exudate profiles and the composition of root-associated bacterial communities. However, it is currently unknown whether disruptions of the JA in the rhizosphere affect root exudation profiles and the relative abundance of bacteria and archaea in the rhizosphere. In the present study, two Arabidopsis mutants that are disrupted in different branches of the jasmonate pathway, namely myc2 and med25, were cultivated in nutrient solution and soil to profile root exudates and bacterial and archaeal communities, respectively. Compared with the wild type, both mutants showed distinct exudation patterns, including lower amounts of asparagine, ornithine, and tryptophan, as well as distinct bacterial and archaeal community composition, as illustrated by an increased abundance of Streptomyces, Bacillus, and Lysinibacillus taxa in the med25 rhizosphere and an Enterobacteriaceae population in myc2. Alternatively, the Clostridiales population was less abundant in the rhizosphere of both mutants. Similarities between plant genotypes were highly correlated, as determined by operational taxonomic units in the rhizosphere and metabolites in root exudates. This strongly suggests that root exudates play a major role in modulating changes in microbial community composition upon plant defense responses.

It has frequently been shown that plants interact with soils to shape rhizosphere microbiomes. However, previous work has not distinguished between effects of soil properties per se, and effects attributable to the resident microbial communities of those soils. We aimed to test whether differences in the structure of bulk soil microbial communities, within a given soil type, would carry over to impact the structure of the rhizosphere microbial community. We used repeated chemical amendments to develop divergent bulk soil microbial community starting points from which rhizosphere development proceeded. Additionally, we contrasted rhizosphere microbiomes associated with two different cultivars of corn (Zea mays). A wide range of bacterial and archaeal taxa responded to chemical resource amendments, which reduced bulk soil microbiome diversities. Corn genotypes P9714XR and 35F40 had largely similar impacts on rhizosphere microbiome development, although significant differences were evident in select treatments. Notably, in cases where resource amendments altered bulk soil microbial community composition, legacy effects persisted into the rhizosphere. Our results suggest that rhizosphere microbial communities may develop into different states depending on site history and prior selective events. This work advances our understanding of soil microbiome dynamics and responsiveness to change in the form of simple resource amendments and the development of the rhizosphere.

Aims The aim of this study was to evaluate effects of PGPR (plant growth-promoting rhizobacteria) isolated from rainforest soil on different plants under limited nitrogen conditions. Methods and Results Bacterial isolates from a Peruvian rainforest soil were screened for plant growth-promoting effects on Arabidopsis (Col-0). Four selected isolates including one Bacillus subtilis, two B. atrophaeus and one B. pumilus significantly promoted growth of Zea mays L. and Solanum lycopersicum under greenhouse conditions. Moreover, the PGPRs significantly promoted growth of S. lycopersicum in both low and nitrogen-amended soil conditions. These PGPR strains were further studied to obtain insights into possible mechanisms of plant growth promotion. Volatile chemicals from those isolates promoted Arabidopsis growth, and the expression of genes related to IAA production was induced in the Arabidopsis plants treated with PGPRs. Further, selected PGPR strains triggered induced systemic resistance (ISR) against Pseudomonas syringae pv tomato DC3000 in Arabidopsis. Conclusions PGPR strains isolated from the rainforest soil promoted the plant growth of Arabidopsis, corn and tomato. Significance and Impact of the Study New PGPR that have wider adaptability to different crops, soils and environmental conditions are needed to decrease our reliance on agricultural amendments derived from fossil-based fuels. The PGPRs isolated from a nonagricultural site constitute new plant growth-promoting strains that could be developed for agricultural uses.

Under environmental conditions, plants are constantly exposed to a wide range of biotic interactions, which include insects, and pathogens. Usually scientists are tempted to study each association individually, which reduces the complexity of the interaction. This restricted view of the problem does not consider that plants are the ballroom in which a multitude of organisms are constantly interacting with each other affecting not only plant responses but also how one organism responds to the other. Plants attacked by insects and pathogens display profound physiological, morphological and chemical changes or adaptations that result in organism attraction or avoidance, depending on the species involved. Therefore, many researchers worldwide have decided to study this phenomenon in a more holistic view, integrating genetics, ecology and physiology to depict these complex interactions. In this review, we will discuss how plant infection by pathogens may affect insect behavior and vice-versa and how plants cope with these multitude of biotic stresses.

Root exudates play important roles in root-soil microorganism interactions and can mediate tripartite interactions of beneficial microorganisms-plant-pathogen in the rhizosphere. However, the roles of organic acid components in this process have not been well studied. In this study the colonization of a plant growth-promoting rhizobacterium, Bacillus amyloliquefaciens SQR9, on cucumber root infected by Fusarium oxysporum f. sp. cucumerinum J. H. Owen (FOC) was investigated. Chemotaxis and biofilm formation response of SQR9 to root exudates and their organic acid components were analysed. Infection of FOC on cucumber had a positive effect (3.30-fold increase) on the root colonization of SQR9 compared with controls. Root secretion of citric acid (2.3 ± 0.2 μM) and fumaric acid (5.7 ± 0.5 μM) was enhanced in FOC-infected cucumber plants. Bacillus amyloliquefaciens SQR9 exhibited enhanced chemotaxis to root exudates of FOC-infected cucumber seedlings. Further experiments demonstrated that citric acid acts as a chemoattractant and fumaric acid as a stimulator of biofilm formation in this process. These results suggest that root exudates mediate the interaction of cucumber root and rhizosphere strain B. amyloliquefaciens SQR9 and enhance its root colonization.

Soil sterilization is often applied in cropping systems to remove soil-borne pathogens and nematodes. In an effort to better understand the role of sterilization on natural microbial communities and resultant plant growth, we examined the interaction between soil sterilization and the growth of three different crops (one native crop, peach; and two non-native crops, corn and tomato) in a soil known to have peach replant disease. Soil sterilization significantly increased plant growth in all crop species. The recovery of the microbial communities following sterilization was dependent upon the presence of a living plant and the final community structure differed between crop species. In all crops grown in the sterilized soil, there were common plant-beneficial microbial functions that were promoted after sterilization: N fixation, P solubilization, biological control, or root growth promotion. Despite the well documented effect of soil sterilization to remove pathogens, it is also a potential means to promote rapid changes in soil microbial communities and the apparent promotion of beneficial microbes as well as a healthier soil microbiome.

There is a concerted understanding of the ability of root exudates to influence the structure of rhizosphere microbial communities. However, our knowledge of the connection between plant development, root exudation and microbiome assemblage is limited. Here, we analyzed the structure of the rhizospheric bacterial community associated with Arabidopsis at four time points corresponding to distinct stages of plant development: seedling, vegetative, bolting and flowering. Overall, there were no significant differences in bacterial community structure, but we observed that the microbial community at the seedling stage was distinct from the other developmental time points. At a closer level, phylum such as Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and specific genera within those phyla followed distinct patterns associated with plant development and root exudation. These results suggested that the plant can select a subset of microbes at different stages of development, presumably for specific functions. Accordingly, metatranscriptomics analysis of the rhizosphere microbiome revealed that 81 unique transcripts were significantly (P

It was hypothesized that disruption of the root–microbiome association creates empty rhizosphere niches that could be filled by both soilborne pathogens and beneficial microbes. The effect of de-coupling root–microbiome associations related to improve soil suppressiveness was investigated in cucumber using the pathogen Fusarium oxysporum f. sp. Cucumerinum (FOC) and its antagonist Bacillus amyloliquefaciens SQR9 (SQR9) system. The root–soil microbiome association of cucumber was disrupted by applying the fungicide carbendazim to the soil, and then FOC or/and its antagonist SQR9 were inoculated in the rhizosphere. In the fungicide treatment, the FOC wilt disease incidence was significantly increased by 13.3 % on average compared to the FOC treatment without fungicide. However, when the fungicide treatment was applied to the soil with SQR9 and FOC, the SQR9 effectively reduced the disease incidence, and improved cucumber plant growth compared to a no fungicide control. These results indicate that de-coupling of root–microbiome associations followed by antagonist inoculation can improve rhizosphere soil suppressiveness, which may help to develop strategies for efficient application of rhizosphere beneficial microbes in agriculture.

Drought is a major constraint on agricultural production. Crop genetic improvement for drought tolerance has received much attention and there is ample information about the ability of specific soil microbes to influence drought tolerance in plants. However, in nature, plants interact simultaneously with an array of beneficial, benign and pathogenic microbes. There is a need to understand the cumulative effect of these multiple interactions on a plant's ability to overcome abiotic stresses such as drought. The objective of this research was to investigate the potential of whole soil microbiomes to help Arabidopsis thaliana plants deal with drought stress under in vivo conditions. A sympatric microbiome (i.e., having a history of exposure to Arabidopsis at a natural site) significantly increased plant biomass under drought conditions, but caused earlier death rates as a consequence of drought; whereas, the two non-sympatric soils did not influence Arabidopsis biomass. Consistent with this, we observed reduced expression levels for several Arabidopsis drought response marker genes (ATDI21, DREB1A, DREB2A, and NCED3) in the sympatric Arabidopsis soil treatment. Pyrosequencing analysis of the three soil microbiomes used in this study identified 84 bacterial OTUs (3% genetic distance) from 41 genera (Burkholderia, Phormidium, Bacillus, Aminobacter, Acidiphilum and among others) that were significantly higher in the sympatric Arabidopsis soil, as compared to the two non-sympatric soils. In conclusion, we have identified a robust set of Arabidopsis-associated microbes that when present in the soil can modify the plant's ability to sense abiotic stress and increase its biomass production.