Decoding Wheat Endosphere–Rhizosphere Microbiomes in Rhizoctonia solani–Infested Soils Challenged by Streptomyces Biocontrol Agents

The endosphere and the rhizosphere are pertinent milieus with microbial communities that perturb the agronomic traits of crop plants through beneficial or detrimental interactions. In this study, we challenged these communities by adding Streptomyces biocontrol strains to wheat seeds in soils with severe Rhizoctonia solani infestation. Wheat plants were grown in a glasshouse standardized system, and the bacterial and fungal microbiomes of 233 samples of wheat roots (endosphere) and rhizosphere soils were monitored for 20 weeks, from seed to mature plant stage. The results showed highly dynamic and diverse microbial communities that changed over time, with Sphingomonas bacteria and Aspergillus, Dipodascus, and Trichoderma fungi increasing over time. Application of biocontrol Streptomyces strains promoted plant growth and maturation of wheat heads and modulated the root microbiome, decreasing Paenibacillus and increasing other bacterial and fungal OTUs. The soils with the highest levels of R. solani had increased reads of Thanatephorus (Rhizoctonia anamorph) and increased root disease levels and increased Balneimonas, Massilia, Pseudomonas, and unclassified Micrococcaceae. As we enter the era of biologically sustainable agriculture, it may be possible to reduce and limit the effects of serious fungal infestations by promoting a beneficial microbiome through the application of biocontrol agents during different periods of plant development.RA was supported by an Endeavour Postdoctoral Fellowship. This study was financed by Grains Research and Development Corporation (GRDC) project no. UF00008

Organic Amendments Alter Soil Hydrology and Belowground Microbiome of Tomato (Solanum Lycopersicum)

Manure-derived organic amendments are a cost-effective tool that provide many potential benefits to plant and soil health. For example, amendment applications may increase soil fertility, improve soil structure, stimulate microbial activity, and suppress plant pathogens. Yet, responses to these applications may have unintended consequences. Inherent variability in the physical, chemical, and biological characteristics of these materials can result in inconsistent outcomes observed after their application. These differences are manifested in plant growth, soil physiochemical properties, and soil microbial community composition. Popular manure-derived organic amendments include dairy manure compost and poultry manure pellets. Dairy manure is an abundant resource on many diversified farms and poultry manure pellets are an economical and commercially available source of nitrogen. Despite a growing body of research demonstrating the plant growth enhancing and disease suppressing potential of vermicompost, its’ relative price and availability has limited its widespread adoption in field-grown vegetable production systems. Additional research which determines how and why vermicompost performs differently than alternative amendments is necessary to justify its greater adoption. A container study was conducted to evaluate how dairy manure compost, dairy manure compost-derived vermicompost, and dehydrated poultry manure pellets impact the tripartite relationship among plant growth, soil physiochemical properties, and microbial community composition. Organic amendments increased soil porosity and soil water holding capacity but delayed plant maturation and decreased plant biomass. Of those treated with organic amendments, vermicompost-amended plants displayed the greatest root growth and overall plant health through time. Distinct microbial communities were detected for each treatment, with an abundance of Massilia, Chryseolinea, Scedosporium, and Acinetobacter distinguishing the control, vermicompost, dairy manure compost, and dehydrated poultry manure pellet treatments, respectively. Known ecological roles of these organisms support the observations made in this study: Massilia and Chryeolinea promote plant growth, Scedosporium abundance reflects the immaturity of the dairy manure compost provided, and Acinetobacter, among several taxa present in the poultry pellet-amended treatment, highlights existing concerns about the safety of poultry manure-based fertilizers in agriculture. This study validates that organic amendments alter the rhizosphere microbiome by influencing plant growth and soil physiochemical properties. In addition, this study highlights the impact of organic amendment application on the physical soil environment and the influence this change has, both directly and indirectly, on soil microbial community composition. Furthermore, this study demonstrates that there is a strong interaction between root growth and the spatial heterogeneity of soil and root-associated microbial communities. The varied response to organic amendment application in this study demonstrates that a more comprehensive characterization of these materials, and their impact on the soil environment, is required to successfully utilize these products in an effort to improve soil health and modify soil microbial communities. While highlighting a widespread need for additional research, this study serves to suggest that vermicompost is a valuable tool to promote plant health and manage disease and supports the adoption of a vermicomposting curing step to stabilize manure-derived fertilizer products

Testing the Proximate Mechanisms for the Process of Character Displacement on the Evolution of Root Traits.

Character displacement, is a process wherein closely resembling species diverge in their resource-linked traits as a response to intense competition. Research evaluating whether character displacement can influence the evolution of a plant’s belowground root system remains unreported in the literature, despite the importance of root systems in capturing resources from the soil environment and mediating belowground competition. Thus, my dissertation addresses the overarching question, Can character displacement influence the evolution of root traits between two closely related species? In the first two data chapters of this dissertation I tested for the potential that root traits can evolve via character displacement using Ipomoea purpurea and I. hederacea. In my first data chapter (Chapter 2) I performed a greenhouse common garden experiment to test if root traits were genetically variable and a competition field experiment to test if belowground competition can impose selection on root traits. In my second data chapter (Chapter 3) I expanded on my findings from Chapter 2 and performed a second competition field experiment to test for the main prediction of character displacement. In addition to the root system, the root-associated microbiome can play a major role in a plant’s realized niche and affect how plants access and compete for belowground resources. Moreover, the root-associated microbiome can potentially influence root phenotypes and vice versa. Consequently, plant-microbe interactions can potentially feedback into plant ecology and evolution and alter the outcome of processes such as belowground plant-plant competition. To this end in my third data chapter (Chapter 4). I asked the broad question, Does the rhizosphere microbial community composition and structure vary with root phenotypes and what are their relative effects on plant fitness according to competitive environment? I subsampled and analyzed the bacterial microbiome from rhizosphere soil taken from individuals of I. purpurea and I. hederacea grown in the presence and absence of belowground competition. I tested if root phenotypes and measures of the rhizosphere microbial community were linked with each other and determined the relative impact of the rhizosphere microbial community on plant fitness in context of belowground competition In brief, my thesis demonstrates that belowgound competition and root traits represent a viable and overlooked agent and target of selection. Most importantly, it demonstrates that belowground competition may potentially result in character convergence, not displacement of root traits. It provides initial evidence for the possibility that the rhizosphere microbiome and root traits can influence each other and effect how plants compete belowground. My work demonstrates the potential for belowground competition to shape plant evolution and diversity and suggests that plant-microbe interactions itself may play an important role in how plants respond and adapt to belowground competition. Collectively, this work represents a novel first step in linking plant ecology and evolution to the ‘hidden’ half.PHDEcology and Evolutionary BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/162871/1/scolom_1.pd

Effects of mass death on community structure and ecosystem function

Death and decomposition are natural processes that are generally well-understood. However, large events of death, such as mass mortality events (MMEs) are increasing in frequency and their impacts on the ecosystem are largely unknown. These events may have both bottom-up effects from increased nutrient input as well as top-down effects from loss of an ecological functional group by the affected population. Different functional MMEs may result in different top-down effects, creating cascading effects. In Chapter 1, I test the hypothesis that scavenger and herbivore simulated MMEs generate novel bottom-up and top-down effects. Results indicate that MMEs have a significant effect on communities, including on soil chemistry, plant tissue, soil microbes, and soil arthropods. Carrion effects on the community were both a result of biomass (MMEs vs. single carcasses) as well as functional group exclusion (herbivores, scavengers). Further, MMEs may also generate long-lasting community effects due to the size and nature of the disturbance. In Chapter 3, I evaluated the potential long-term of effects of MMEs by sampling an experimental MME that was conducted four years earlier. I found that MMEs generated long-term asymmetrical effects on ecosystems, with some noticeable changes in increased soil nutrients as well as an unexpected effect of biomass on aboveground arthropod communities, with very little effect on belowground soil arthropods. However, studies of long-term decomposition from mass carcasses may expand beyond studying MMEs. Composting of carrion is a continuous disturbance event, with numerous carcasses being deposited in the same location over a longer period of time. In Chapter 2, I analyzed potential effects on the surrounding community at a unique instance of concentrated carcass disposal (5 years old). Significant differences were revealed between samples taken near the compost pit (0 m, 5 m) compared to further distances (10 m, 25 m, 50 m) with calcium being increased away from the pit, different soil microbial communities at the pit than farther distances and increased aboveground arthropod abundance at the pit. These experiments provide us with a greater, holistic understanding of previously understudied events of mass death on community structure and ecosystem function

Studies on the host-pathogen interactions for Rhizoctonia solani AG2-1 causing damping-off disease of Brassica napus (Oilseed Rape)

Rhizoctonia solani is a necrotrophic soil-borne plant pathogen species complex, of which anastomosis group (AG) 2-1 causes devastating disease on oilseed rape (OSR, Brassica napus). It is frequently isolated from arable crop fields where it affects establishment and yield via pre- and post-emergence damping off, hypocotyl and root rot. Genetic resistance to R. solani AG2-1 has not been observed and long-lived sclerotia, plus a broad host range allow the pathogen to survive in the soil for many years. Here, the interactions between Rhizoctonia solani AG2-1, its crop host OSR and the model organism Arabidopsis thaliana were explored. Variation in responses to R. solani were observed between commercial OSR varieties and gene expression data showed that susceptibility was associated with auxin and abscisic acid signalling, and the MYC2 branch of jasmonate signalling, while reactive oxygen species, ethylene signalling and the ERF/PDF branch of jasmonate signalling were associated with increased tolerance. This was supported by inoculation of A. thaliana defence mutants and microscopy using Jas9:VENUS and IAA2pro:GUS lines. Further investigations into the role of auxins in R. solani AG2-1 – A. thaliana interactions showed that R. solani was able to differentially affect the root architecture of WT and aux1 transport mutants. Experiments showing the effects of 2,4-D, PAA and NAA demonstrated that PAA was able to restore gravitropism in aux1. R. solani produced both IAA and PAA when grown in broth culture and growth stimulation was observed when R. solani was grown in broth with low concentrations of exogenous PAA. Analysis of gene expression markers (GEMS) from a previous genome wide association study (GWAS) provided further evidence for the involvement of auxins, jasmonates and ethylene in the defence responses of OSR to R. solani AG2-1. Corresponding A. thaliana candidate gene mutants were inoculated with R. solani AG2-1 under experimental conditions to identify potential susceptibility genes. Two of these were taken further and B. rapa TILLING line resources were developed. This thesis increases understanding of the defence pathways involved in resistance and susceptibility to R. solani AG2-1, examines the influence that R. solani has on the root architecture of auxin mutants, and provides candidate gene TILLING line resources for future work

Studies on the host-pathogen interactions for Rhizoctonia solani AG2-1 causing damping-off disease of Brassica napus (Oilseed Rape)

Rhizoctonia solani is a necrotrophic soil-borne plant pathogen species complex, of which anastomosis group (AG) 2-1 causes devastating disease on oilseed rape (OSR, Brassica napus). It is frequently isolated from arable crop fields where it affects establishment and yield via pre- and post-emergence damping off, hypocotyl and root rot. Genetic resistance to R. solani AG2-1 has not been observed and long-lived sclerotia, plus a broad host range allow the pathogen to survive in the soil for many years. Here, the interactions between Rhizoctonia solani AG2-1, its crop host OSR and the model organism Arabidopsis thaliana were explored. Variation in responses to R. solani were observed between commercial OSR varieties and gene expression data showed that susceptibility was associated with auxin and abscisic acid signalling, and the MYC2 branch of jasmonate signalling, while reactive oxygen species, ethylene signalling and the ERF/PDF branch of jasmonate signalling were associated with increased tolerance. This was supported by inoculation of A. thaliana defence mutants and microscopy using Jas9:VENUS and IAA2pro:GUS lines. Further investigations into the role of auxins in R. solani AG2-1 – A. thaliana interactions showed that R. solani was able to differentially affect the root architecture of WT and aux1 transport mutants. Experiments showing the effects of 2,4-D, PAA and NAA demonstrated that PAA was able to restore gravitropism in aux1. R. solani produced both IAA and PAA when grown in broth culture and growth stimulation was observed when R. solani was grown in broth with low concentrations of exogenous PAA. Analysis of gene expression markers (GEMS) from a previous genome wide association study (GWAS) provided further evidence for the involvement of auxins, jasmonates and ethylene in the defence responses of OSR to R. solani AG2-1. Corresponding A. thaliana candidate gene mutants were inoculated with R. solani AG2-1 under experimental conditions to identify potential susceptibility genes. Two of these were taken further and B. rapa TILLING line resources were developed. This thesis increases understanding of the defence pathways involved in resistance and susceptibility to R. solani AG2-1, examines the influence that R. solani has on the root architecture of auxin mutants, and provides candidate gene TILLING line resources for future work

Unravelling Micromonospora interactions with its host plant and the associated microbioma

[ES] La Unión Europea depende en gran medida de las importaciones de soja (> 70%) como fuente de proteínas, ya que la producción local apenas cubre el 5% de la demanda interna. Por ello, es necesario explorar fuentes alternativas para reducir esta dependencia. Entre las leguminosas, Lupinus angustifolius es una opción dado su alto valor proteico y su uso para la alimentación animal y humana. Esta leguminosa es una planta autóctona del continente europeo, que está bien adaptada a las condiciones climáticas de otras regiones como puede ser Australia o América. También crece de forma silvestre en suelos pobres gracias a su capacidad para fijar nitrógeno en simbiosis con bacterias. La adaptación de dicha planta puede deberse en parte a los microorganismos asociados a sus raíces, que le proporcionan estabilidad y resistencia, además de moléculas promotoras del crecimiento vegetal y nutrientes. Las comunidades microbianas asociadas a las plantas se ven influenciadas por diversos factores como son el genotipo/especie del huésped, el tipo de suelo, compartimento de la planta y estación climática, entre otros. Separar estos factores para saber cuáles son los que más influyen en la asociación de microorganismos a las plantas es una tarea muy complicada puesto que ninguno se da de forma independiente. En el primer capítulo de esta tesis doctoral, se abordó esta temática estudiando las variaciones estacionales y geográficas de la microbiota del suelo, y caracterizando el microbioma asociado a la planta Lupinus angustifolius en diferentes condiciones de cultivo mediante técnicas independientes de cultivo. En el segundo capítulo, el objetivo fue el aislamiento e identificación molecular de la comunidad bacteriana presente en los distintos tejidos de la planta y la generación de una colección de cepas asociada al microbioma de L. angustifolius. Con los resultados obtenidos en los dos primeros capítulos, se describió por primera vez el microbioma core de la planta L. angustifolius. En el tercer y último capítulo de esta tesis doctoral se trató de descifrar las interacciones de Micromonospora con su planta huésped y el microbioma asociado, empleando para tal fin la información obtenida en los capítulos anteriores. Se desarrollaron siete comunidades sintéticas que se inocularon en experimentos in planta, en condiciones de invernadero en un suelo con su comunidad natural, y en un sistema gnotobiótico con un sustrato estéril. Posteriormente se evaluó mediante técnicas independientes de cultivo cómo se ensamblaban los microorganismos a la raíz y cuál era el efecto de las distintas SynComs en la planta huésped y el microbioma circundante. [EN] The European Union highly depends on soy imports (> 70%) as a protein source since local production barely covers 5% of its internal demand. Thus, it is necessary to explore alternative sources to reduce this dependency. Among legumes, Lupinus angustifolius is an important alternative given its high protein value and use for animal and human nutrition. This legume is a native plant of Europe, well adapted to the climatic conditions of many countries. It also thrives in poor soils due to its capacity to fix nitrogen. Plant adaptation may be partly due to the microorganisms associated with its roots, providing stability and resilience, in addition to plant growth promoting molecules and nutrients. Plant-associated microbial communities are influenced by several factors such as host genotype/species, soil type, plant compartment and climatic season, among others. Separating these factors to understand which are the most influential in the association of microorganisms to plants is a very complex task as they do not occur independently. In the first chapter of this doctoral thesis, this topic was addressed by studying seasonal and geographical variations in the soil microbiota, and characterizing the microbiome associated with the plant Lupinus angustifolius under different cultivation conditions using an independent culture methodology. The results of the soil samples analysed suggest that the difference in the microbial community composition observed between the two sampling locations, Cabrerizos and Salamanca, was partly due to differences in soil conditions. None of the communities analysed (bacterial and fungal) showed differences in alpha diversity (Shannon index) between the climatic seasons in which the samples were collected. Beta diversity (Bray-Curtis-based principal coordinate analysis) for both microbial communities separated the samples into two groups according to soil type. In the case of bacteria, it was observed that, in addition, subgroups were formed according to the climatic seasons for the Salamanca soil. Interestingly, this also occurred with the fungal communities, where the samples were separated by season in both soil types. These results suggest that the main difference in soil microbial communities is due to edaphic properties, although environmental factors such as temperature, humidity or rainfall also influence the diversity of soil microbial communities. In addition, the microbiome associated with the legume Lupinus angustifolius cultivated under natural and greenhouse conditions was also characterized. For this purpose, wild and greenhouse-grown plants were collected from the same locations and analysed by 16S rRNA gene and ITS-2 gene profiling. Bacterial communities were characterized in the different plant compartments (rhizosphere, roots, nodules and leaves) while ITS profiles were restricted to the soil and rhizosphere. As previously reported for other plants, the highest richness was found in the rhizosphere, followed by the roots, leaves, and nodules. Within the rhizosphere, the bacterial richness in the in Salamanca plants was lower, especially for the field samples, probably affected by a pH below 7 and high amounts of P and K. In general, the compartments from the plants grown under greenhouse conditions showed a slightly higher bacterial diversity when compared to the wild plants. Within the fungal communities, the Shannon index was significantly higher in soil than rhizosphere samples (P1% and designed several isolation protocols. A total of 722 bacterial strains were isolated. As expected, the highest number of isolates was obtained in the rhizosphere compartment and a similar pattern was observed with a decreasing diversity gradient starting from the rhizosphere followed by the roots, leaves and nodules. In total, 87 different genera were identified, of which 19 had more than 10 isolates. The most abundant strains were identified in the genera Pseudomonas, Streptomyces, Agrobacterium, Bacillus and Pseudoclavibacter. In this work, 51.9% of the searched genera were isolated, and 74.7% of the isolated genera were identified by metagenomics, but 19.6% could not be detected in any plant compartment by metagenomics. Plant pathogenicity assays showed that 29% of the L. angustifolius isolates were potentially pathogenic for Arabidopsis thaliana Col-0. In turn, 394 strains (55%) were found to be non-pathogenic and 116 (16%) promoted the growth of A. thaliana. Analysis of metagenomics and culturomics results identified a core microbiome of the host plant L. angustifolius that included Acidovorax, Bradyrhizobium, Caulobacter, Chitinophaga, Flavobacterium, Kribella, Massilia, Pseudomonas, Pseudoxanthomonas, Rhizobium, Sphingomonas, Streptomyces and Variovorax. The composition and diversity of the identified host plant-associated bacteriome varied slightly between sampling locations and growing conditions. The genera identified as the core microbiome were present in more than 80% of the samples analysed. In chapter three of this work, the aim was to decipher the interactions of Micromonospora with its host plant and the associated microbiome, using the information obtained in the previous two chapters. Seven different synthetic communities (SynComs) were designed using bacterial strains isolated from the rhizosphere and roots of L. angustifolius to study their effect on the root and rhizosphere of the plant. In addition, we wanted to learn if the selected strains had any effect on the host plant and the natural bacterial communities present in the cultivation soils. After obtaining the genomes of the bacterial strains included in the different SynComs, a comparative genomic analysis was carried out, confirming that all the selected strains had genes with functions related to plant association and growth promotion. Plants were grown for 8 weeks in unsterilised soil under greenhouse conditions, and several plant parameters were measured and compared against the control plants (uninoculated). The plants inoculated with SynCom_7 showed the best growth and development. Furthermore, 16S rRNA gene profiling showed that the soil samples were the most diverse, followed by rhizosphere and roots (alpha diversity) (Figs. 54 and 55). Beta diversity grouped the samples into three clusters according to compartments: soil, rhizosphere and roots. In addition, a clustering pattern was observed for the SynComs inoculated in the root samples. All consortia that contained the nitrogen fixer, Bradyrhizobium sp. in the synthetic community formed one cluster, while the rest of the SynComs were recovered in a second cluster. The analysis of the bacterial composition of the bulk soil samples confirmed that the synthetic communities did not affect the composition of the soil where the plant was growing. However, when we studied the bacterial composition in the rhizosphere, a slight variation was observed, and the bacterial community of root samples was greatly influenced by the inoculated SynComs. The second part of this chapter consisted in the evaluation of the different SynComs on L. angustifolius plants grown in sterile soil under a gnotobiotic system. As in the first experiment, several growth parameters were registered, observing that plants inoculated with SynCom_7 showed the highest growths, again. Pseudomonas sp. Strain CRA141 showed the closest association with the roots. This result is not unexpected as it is well known that many Pseudomonas strains associate to plant roots. In addition, it was found that Micromonospora sp. Lupac 08 was detected in the rhizosphere and roots, and while this actinobacterium is not part of the core microbiome, it could be considered a "satellite" microorganism with important beneficial functions for the plant. Plant gene expression was related to the effect of the SynComs inoculated. When inoculated consortia included the Bradyrhizobium strain, very little differences were found when compared to the control plants, however, when only the Micromonospora strain and/or the other members of the SynComs were added, the differential gene expression increased threefold (Fig. 62). Gene ontology enrichment analyses revealed that those functions that were enriched by inoculating the different SynComs were clearly related to plant-microbe interaction functions. The same was observed for the enriched metabolic pathways when KEGG analysis was performed

Microbiome assembly, dynamics, and recruitment within the wheat

Wheat is a staple crop for 40% of the global population. However, yields over the remainder of the 21st century will become strained by climate change, necessitating new innovations to maintain and increase productivity. Root associated microbial communities have demonstrated the capacity to improve yields by increasing nutrient bioavailability, alleviating abiotic stress, and providing disease protection. This project aimed to characterise the microbial community associated with wheat, to identify core microbial taxa associated with the roots, thus likely to provide benefits to the host. This project also aimed to understand which factors influence the microbiome, and which of these taxa utilise host derived carbon. 16S rRNA gene and ITS2 region metabarcoding of the bacterial, fungal, and archaeal communities within the rhizosphere and endosphere of wheat revealed that soil type had a major impact on the community composition, whilst plant genotype had a limited effect on the microbiome. Five core bacterial families were enriched within the rhizosphere or endosphere of wheat regardless of soil type or genotype, Streptomycetaceae, Burkholderiaceae, Pseudomonadaceae, Rhizobiaceae, and Chitinophagaceae. Streptomycetaceae and Burkholderiaceae were the most abundant families within the endosphere. Full length 16S rRNA gene sequencing resolved these groups to the species or genus level. Developmental senescence was shown to negatively impact the abundance of these groups, demonstrating input from the living plant is required to maintain their presence within the endosphere. Stable isotope probing showed nine bacterial taxa utilised host derived carbon, including Pseudomonadaceae and Burkholderiaceae. Overall, this project has provided significant progress towards our understanding of the core bacterial families associated with wheat roots. This can be followed up with investigations into the roles these microbes play within the root, and how they interact with the host. In the future this understanding could lead to new ways of utilising the capabilities of the microbial community for agriculture

Roles and recruitment of Streptomyces species in the wheat root microbiome.

The demand for staple food crops is rising alongside the world’s population and matching supply to demand is one of the greatest challenges facing global food security. A key strategy is to better understand and exploit microorganisms that associate with plant roots, thus improving growth and reducing the incidence of disease. Streptomyces is a genus of bacteria that are consistently found in soil and are well known for their diverse and specialised metabolism. A growing body of literature documents their association with higher Eukaryotes, including plants. Their ability to improve plant growth by alleviating stress and reducing disease has been documented, but factors determining their recruitment are enigmatic. Many Streptomyces spp. produce specialised metabolites that kill the wheat take-all fungus, G. tritici, but it is not known how widespread this trait is. This study shows that at least 17 out of 54 streptomycetes (31%) isolated from wheat roots can inhibit the growth of wheat take-all fungus. Isolates from the Paragon variety showed greater antifungal activity which may implicate host genotype with functional variation of the root microbiome. The genomes of two Streptomyces strains with exceptionally potent antifungal activity were sequenced and putative antifungal gene cluters were identified. Root exudates are hypothesised to play a key role in the recruitment of beneficial microbes and 13CO2 DNA stable isotope probing (SIP) experiment revealed that many of the rhizosphere enriched bacterial taxa utilised wheat root exudates. Surprisingly, Streptomycetaceae were not metabolising root exudates in the rhizosphere but the data suggested that are feeding on plant metabolites in the endosphere, where they have less competition. Whole bacterial community analysis showed their abundance was significantly enriched in the endosphere compartment. Nitric oxide (NO) was implicated for the first time in the recruitment of Steptomyces bacteria to the plant rhizosphere using S. coelicolor as a model. Mutant strains with deletions in genes coding for NO detoxification colonised the rhizosphere better than the control, while bulk soil was survival was unaffected, suggesting NO enhances root colonisation by these bacteria. Overall, this research gives new insight into the ecological roles of Streptomyces spp. and supports the hypothesis that they are useful plant growth promoting bacteria that could be exploited as plant probiotics