O crescente aumento da população acarretará uma alteração na demanda por alimentos, tornando-se assim motivo de preocupação no âmbito da produção agrícola mundial, As mudanças climáticas constituem uma das mais sérias variáveis que podem prejudicar o processo produtivo de diferentes culturas de importância econômica, pois tais condições têm alterado o cenário ambiental global, tornando o estresse hídrico uma questão importante em todo o mundo. Esta condição tem sido apontada como um problema para o aumento produtivo de diferentes culturas. Assim, novas soluções para a sobrevivência e o crescimento das plantas sob a disponibilidade restrita de água são de importância central para maior eficiência agrícola. O uso de microrganismos simbióticos como inoculantes em culturas agrícolas pode contribuir com o sucesso desta atividade, pois diversos trabalhos têm relatado a presença de mecanismos adaptados a condições extremas podendo ser utilizados como ferramentas alternativas para aumentar a tolerância a seca das culturas que estarão associadas. Neste contexto, a busca por microrganismos com capacidade de sobrevivência em ambientes extremos, tem se apresentado como uma estratégia favorável na busca de opções para resolução destes problemas. Entretanto, pouco se sabe sobre bactérias simbióticas com a soja e os efeitos deste quando em condições de estresse hídrico. Desta forma, propõe-se com este estudo a descoberta de linhagens compatíveis que promovam crescimento de plantas de soja sob estresse hídrico e elucidação dos mecanismos que essas bactérias utilizam para induzir tolerância ao estresse. Dentro dessa abordagem, visa-se ainda o desenvolvimento de inoculante bacteriano em consórcio capaz de promover o crescimento e aumentar a produtividade de plantas da soja sob condições limitantes de água. / The increasing population will lead to a change in the demand for food, making it a major concern in the field of world agricultural production. Climate change is one of the most serious variables that can hinder the productive process of different crops of economic importance. such conditions have altered the global environmental scenario, making water stress an important issue throughout the world. This condition has been pointed out as a problem for the productive increase of different cultures. Thus, new solutions for the survival and growth of plants under the restricted availability of water are of central importance for greater agricultural efficiency. The use of symbiotic microorganisms as inoculants in agricultural crops may contribute to the success of this activity, since several studies have reported the presence of mechanisms adapted to extreme conditions and can be used as alternative tools to increase the drought tolerance of the crops that will be associated. In this context, the search for microorganisms with the ability to survive in extreme environments has been presented as a favorable strategy in the search for options to solve these problems. However, little is known about symbiotic bacteria with soybean and its effects when under stress conditions. Thus, it is proposed with this study the discovery of compatible strains that promote the growth of soybean plants under water stress and elucidation of the mechanisms that these bacteria use to induce tolerance to stress. Within this approach, the development of a bacterial inoculant in a consortium capable of promoting growth and increasing the productivity of soybean plants under water limiting conditions.

O crescente aumento da população acarretará uma alteração na demanda por alimentos, tornando-se assim motivo de preocupação no âmbito da produção agrícola mundial, As mudanças climáticas constituem uma das mais sérias variáveis que podem prejudicar o processo produtivo de diferentes culturas de importância econômica, pois tais condições têm alterado o cenário ambiental global, tornando o estresse hídrico uma questão importante em todo o mundo. Esta condição tem sido apontada como um problema para o aumento produtivo de diferentes culturas. Assim, novas soluções para a sobrevivência e o crescimento das plantas sob a disponibilidade restrita de água são de importância central para maior eficiência agrícola. O uso de microrganismos simbióticos como inoculantes em culturas agrícolas pode contribuir com o sucesso desta atividade, pois diversos trabalhos têm relatado a presença de mecanismos adaptados a condições extremas podendo ser utilizados como ferramentas alternativas para aumentar a tolerância a seca das culturas que estarão associadas. Neste contexto, a busca por microrganismos com capacidade de sobrevivência em ambientes extremos, tem se apresentado como uma estratégia favorável na busca de opções para resolução destes problemas. Entretanto, pouco se sabe sobre bactérias simbióticas com a soja e os efeitos deste quando em condições de estresse hídrico. Desta forma, propõe-se com este estudo a descoberta de linhagens compatíveis que promovam crescimento de plantas de soja sob estresse hídrico e elucidação dos mecanismos que essas bactérias utilizam para induzir tolerância ao estresse. Dentro dessa abordagem, visa-se ainda o desenvolvimento de inoculante bacteriano em consórcio capaz de promover o crescimento e aumentar a produtividade de plantas da soja sob condições limitantes de água. / The increasing population will lead to a change in the demand for food, making it a major concern in the field of world agricultural production. Climate change is one of the most serious variables that can hinder the productive process of different crops of economic importance. such conditions have altered the global environmental scenario, making water stress an important issue throughout the world. This condition has been pointed out as a problem for the productive increase of different cultures. Thus, new solutions for the survival and growth of plants under the restricted availability of water are of central importance for greater agricultural efficiency. The use of symbiotic microorganisms as inoculants in agricultural crops may contribute to the success of this activity, since several studies have reported the presence of mechanisms adapted to extreme conditions and can be used as alternative tools to increase the drought tolerance of the crops that will be associated. In this context, the search for microorganisms with the ability to survive in extreme environments has been presented as a favorable strategy in the search for options to solve these problems. However, little is known about symbiotic bacteria with soybean and its effects when under stress conditions. Thus, it is proposed with this study the discovery of compatible strains that promote the growth of soybean plants under water stress and elucidation of the mechanisms that these bacteria use to induce tolerance to stress. Within this approach, the development of a bacterial inoculant in a consortium capable of promoting growth and increasing the productivity of soybean plants under water limiting conditions.

Although plant growth-promoting rhizobacteria (PGPR) have shown tremendous potential to be used as inoculants for many agricultural crops, they may not survive severe environmental conditions in the field which could limit their large scale applications. Endophytic bacteria, which can be recovered from inside plant tissues such as roots, stems and leaves, might overcome this limitation due to their unique ecological niche inside plant roots where they are sheltered from external environmental disturbances. Some of these bacterial endophytes have beneficial effects on their host plants and stimulate plant growth or reduce disease symptoms, apparently through mechanisms that are similar to those proposed for PGPR. The objective of this study was to assess a collection of endophytic bacteria for PGPR traits and potential use to enhance the rhizobial-legume symbiosis. Forty isolates obtained from the roots of various plants were identified by fatty acid methyl ester (FAME) analysis, and 16S RNA gene sequencing analysis. The majority (i.e., 75%) were identified as Pseudomonas species. Many of these isolates were able to solubilize phosphate, produce indole-3-acetic acid (IAA), produce aminocyclopropane-1-carboxylic acid (ACC) deaminase, synthesize siderophores and show antagonistic activities against several soil-borne plant pathogenic fungi under in vitro conditions. Selected isolates were further evaluated for the ability to enhance plant growth and nodulation of alfalfa when co-inoculated with Sinorhizobium meliloti under growth chamber conditions using growth pouch and potted soil assays. Results revealed that P. putida strain EB EE 4-25, P. syringae strain EB XDE 4-48, and P. fluorescens strain EB EE 2-23 significantly increased shoot length, root length, enhanced nodulation and increased lateral root formation of alfalfa plants in growth pouch and potted soil assays when co-inoculated with S. meliloti strain P102 compared to plants inoculated with S. meliloti strain P102 alone. Results also suggested that expression of one or more of the mechanisms, such as solubilization of phosphate, production of IAA, production of siderophores, and ACC deaminase production might have played a role in the enhancement of the alfalfa- Sinorhizobium symbiosis. These results suggest that some endophytic bacterial strains may be useful as biofertilizers and/or biocontrol agents in sustainable agricultural practices.

Although plant growth-promoting rhizobacteria (PGPR) have shown tremendous potential to be used as inoculants for many agricultural crops, they may not survive severe environmental conditions in the field which could limit their large scale applications. Endophytic bacteria, which can be recovered from inside plant tissues such as roots, stems and leaves, might overcome this limitation due to their unique ecological niche inside plant roots where they are sheltered from external environmental disturbances. Some of these bacterial endophytes have beneficial effects on their host plants and stimulate plant growth or reduce disease symptoms, apparently through mechanisms that are similar to those proposed for PGPR. The objective of this study was to assess a collection of endophytic bacteria for PGPR traits and potential use to enhance the rhizobial-legume symbiosis. Forty isolates obtained from the roots of various plants were identified by fatty acid methyl ester (FAME) analysis, and 16S RNA gene sequencing analysis. The majority (i.e., 75%) were identified as Pseudomonas species. Many of these isolates were able to solubilize phosphate, produce indole-3-acetic acid (IAA), produce aminocyclopropane-1-carboxylic acid (ACC) deaminase, synthesize siderophores and show antagonistic activities against several soil-borne plant pathogenic fungi under in vitro conditions. Selected isolates were further evaluated for the ability to enhance plant growth and nodulation of alfalfa when co-inoculated with Sinorhizobium meliloti under growth chamber conditions using growth pouch and potted soil assays. Results revealed that P. putida strain EB EE 4-25, P. syringae strain EB XDE 4-48, and P. fluorescens strain EB EE 2-23 significantly increased shoot length, root length, enhanced nodulation and increased lateral root formation of alfalfa plants in growth pouch and potted soil assays when co-inoculated with S. meliloti strain P102 compared to plants inoculated with S. meliloti strain P102 alone. Results also suggested that expression of one or more of the mechanisms, such as solubilization of phosphate, production of IAA, production of siderophores, and ACC deaminase production might have played a role in the enhancement of the alfalfa- Sinorhizobium symbiosis. These results suggest that some endophytic bacterial strains may be useful as biofertilizers and/or biocontrol agents in sustainable agricultural practices.

Magister Scientiae - MSc (Biotechnology) / Endophytic bacteria are known to have an endosymbiotic relationship with plants and provide them with many beneficial properties. These bacteria stimulate plant hormones, provide protection from pathogens and increase nutrient availability in the environment. In this study some of these potential growth factors were tested. Endophytic bacteria have the potential to be of great value for the increase of crop production. They offer a variety of processes that aid in plant growth promotion in an ecofriendly manner. The use of endophytic bacteria provides a cheaper and cleaner approach compared to industrial made fertilizers. They also have potential uses in bioremediation to clean the environment polluted by industrial processes. Endophytes were isolated and showed significant growth improvement. Each isolate displayed different morphologies. Isolates were tested for classical growth promotion mechanisms such as the ability to solubilize phosphate, Indole-3-acetic acid and siderophore production. Inductively Coupled Plasma Optical Emission Spectrometry was performed to measure the effect of the isolates on the plants nutrient profile. The isolates were then tested again while the plants were under heavy metal stress to determine if they were still capable of growth promotion. The plants were then assayed for cell death using Evans blue and biomass was measured to determine the effect of vanadium stress. Inductively Coupled Plasma Optical Emission Spectrometry was performed again to assess the change in nutrient profile while under vanadium stress. / 2021-08-31

The US Department of Energy has focused research efforts on developing switchgrass into a bioenergy feedstock, helping to offset the use of non-renewable fossil fuels and make the US more energy independent. Bacterial endophytes, which reside inside plant tissues, are proven to increase yield and stress resistance in a number of plants. The primary objective of this dissertation was to explore the use of endophytes to improve biomass yields of switchgrass on lands not suitable for food crops and better understand the underlying mechanisms of the plant-endophyte interaction. Integration of this research into K-12 STEM education to increase interest in plant sciences and create the next generation of scientists with the motivation to help solve the challenges facing society in the twenty first century was the objective of the outreach component of this project. Chapter one demonstrates the ability of Burkholderia phytofirmans strain PsJN to colonize switchgrass and promote plant growth under in vitro (approximately 50% higher), and growth chamber and greenhouse (48.6% higher biomass yields) conditions. The objectives of Chapter two were to determine stand establishment in the field with different nutrient levels. PsJN bacterization positively benefited growth and development of switchgrass seedlings in the field with both low and high nutrient content. Highly significant (p<0.001) stimulation of root and shoot growth, lateral root formation and number of tillers was recorded on soil with low fertility. PsJN bacterization also enhanced biomass accumulation during the two seasons of growth on both poor (p<0.001) and rich (p<0.05) soil, indicating the potential for the use of PsJN in a low-input switchgrass feedstock production system. Chapter three outlines differences in gene expression patterns upon bacterization, between the responsive cv. Alamo, and a non-responsive cv. Cave-in-Rock. Using EST microarrays and quantitative PCR up- and down-regulated genes were identified in both cultivars. One of the key genes identified was a member of the tau class, glutathione S-transferase (GST). GST enzymes are known to be involved in plants responses to stress. Using overexpression and knockout/knockdown techniques we demonstrated that GST is likely involved in the bacterization induced early plant growth promotion in switchgrass. Chapter four describes the potential for the utilization of beneficial bacterial endophytes capable of fixing atmospheric nitrogen in a free-living state in the development of low-input switchgrass feedstock production systems. Sphingomonas sp. strain NSL isolated from switchgrass tissue was able to grow on nitrogen free medium and stimulated growth of switchgrass cv. Alamo under nitrogen deficient conditions. The ability to fix atmospheric nitrogen was also moved to Burkholderia phytofirmans strain PsJN via horizontal gene transfer from the legume nodulating Burkholderia phymatum. The transformed PsJN was able to fix nitrogen and promote plant growth under nitrogen limited conditions. At every step of the research described in this dissertation efforts were made to include its elements into K-12 education. Chapter five describes four case studies aiming at the enhancement of youth interest in plant sciences in the socieoeconomically depressed areas of Southside Virginia. / Ph. D.

Expanding global populations, unequal food distribution and disease pressure suggest food poverty is increasing. Consequently, much attention is focussed on alternative natural methods in which to increase agricultural yield. Previously, it was observed that Trichoderma hamatum strain GD12 and its respective N-acetyl-β-D-Glucosamine mutant ∆Thnag:hph promoted plant biomass and fitness that, as a result, may provide a credible natural alternative to synthetic fertilisers. However, on a molecular level, the manner in which this is achieved has not been fully elucidated. In this thesis, I report the biofertiliser effect of GD12 and mutant ∆Thnag::hph once applied to autoclaved peat microcosms as sole applications. Furthermore, I demonstrate the biocontrol ability of GD12 when co-inoculated with Sclerotinia sclerotiorum or Rhizoctonia solani and reveal, that once mycelium co-inoculation has occurred, GD12 increase plant biomass and provide protection; whilst ∆Thnag::hph does not. Consequently, I challenged the biocontrol effects of Trichoderma metabolite extract where I validate that both Trichoderma wild type GD12 and mutant ∆Thnag::hph are incapable of suppressing pathogen growth. Subsequently, I characterised the up-regulated signatures associated with GD12 and ∆Thnag::hph using LC-MS techniques where unique compounds were discovered from each strain of Trichoderma. In conclusion, I provide evidence that N-acetyl-β-D-Glucosamine mutation bring about metabolomic changes that affect the fungal secretome which, in turn, alters plant phenotype, fitness and germination. Furthermore, I have shown that these effects are species specific and depend upon pathogen, plant and fungal properties. However, further investigations are needed to fully elucidate the compound(s) responsible for biocontrol and biofertilisation; especially plant-specific effects that take place as a consequence of fungal activity.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: In order to test the effect of different plant growth-promoting strategies on Triticum aestivum L. (wheat), we investigated the ability of biochar and a grain-associated soil yeast, to improve the growth of this crop. Our first goal was to study the effect of biochar amendments to sandy soil on the growth and nutrition of wheat in the presence of mycorrhizal fungi. This was accomplished by amending soil with 0%, 1%, 2.5%, 5% and 10% (w/w) biochar and cultivating wheat plants in these soil-biochar mixtures. After harvesting, plant growth and mycorrhizal colonization of roots were measured. In addition, we studied the nutritional physiology of these plants with regards to nitrogen (N), phosphorous (P) and potassium (K) concentrations, as well as the growth efficiencies and uptake rates of these nutrients. We found that wheat growth was improved by biochar amendments to soil, probably as a result of elevated K levels in the plant tissues supplied by the biochar amendments. The second goal of this study was to obtain a soil yeast from the rhizosphere of another monocot in the family Poaceae, i.e. Themeda triandra Forssk. (red grass), and then evaluate this isolate for its ability to improve wheat performance. Three different Cryptococcus species were isolated from the rhizosphere of wild grass, i.e. Cryptococcus zeae, Cryptococcus luteolus and Cryptococcus rajasthanensis. Since C. zeae was previously isolated from maize, an isolate representing this species was selected to be used in further experimentation. With the ultimate goal of testing the ability of this yeast to improve wheat growth, its effect on wheat germination was investigated and compared to that of two other soil yeasts, i.e. Cryptococcus podzolicus CAB 978 and Rhodotorula mucilaginosa CAB 826. These three yeasts were subsequently tested for their ability to improve wheat growth in pot cultures in a greenhouse. After one and two months of growth, the culturable yeasts present in the rhizosphere and bulk soil were enumerated. The effects of these yeasts were elucidated by measuring wheat growth in terms of dry weight, as well as root and shoot relative growth rates (RGR). Changes in wheat nutrition were evaluated by determining the concentrations, growth efficiencies and uptake rates for P, K, zinc (Zn) and iron (Fe). During this study, it was found that only C. zeae CAB 1119 and C. podzolicus CAB 978 were able to enhance seed germination. Similarly, it was shown that C. zeae CAB 1119 was able to improve wheat growth during the first and second month of cultivation, whereas C. podzolicus CAB 978 only improved growth during the first month, and R. mucilaginosa CAB 826 had no effect on growth. This improved growth could be attributed to C. zeae CAB 1119 improving the P, K, Zn and Fe growth efficiency of wheat, which positively influenced the root and shoot RGR, and subsequently wheat growth. Our final goal was to test whether C. zeae CAB 1119 could affect wheat growth and nutrition when cultivated in sandy soil, which contained natural microbial consortia and 10% (w/w) biochar. Plants treated with viable or autoclaved cells of C. zeae CAB 1119, were subsequently cultivated in soil only or soil amended with biochar. After one month, plants were harvested and growth was measured with regards to dry weight, root RGR and shoot RGR. In addition, the concentrations of P, K, Zn and Fe were analyzed for these plants, where after the growth efficiencies and uptake rates were calculated for these four nutrients. Results indicated that plants growing in soil amended with biochar, and treated with viable C. zeae CAB 1119, showed the best growth. The increased root and shoot RGR witnessed in these plants was probably due to increased concentrations of P and K in the plants. This study opens new avenues of research with regards to the bio-fertilizers of wheat. / AFRIKAANSE OPSOMMING: Die uiteindelike doel van die studie was om die effek van verskillende plantgroei bevorderende metodes op die groei van Triticum aestivum L. (koring) te ondersoek. Dus het ons die vermoë van houtskool en ‘n graan-geassosieerde grondgis getoets om die groei van dié plant te bevorder. Die eerste doel van die studie was om die effek van houtskool toedienings tot sanderige grond te evalueer. Dit is bewerkstellig deur 0%, 1%, 2.5%, 5% en 10% (w/w) van die houtskool by die sand toe te voeg en koring in die houtskool-sand mengsels te kweek. Na die verlangde groei tydperk is die koring geoes en die mikorrizale kolonisasie op en in die koring wortels bepaal. Gedurende hierdie studie is die effek van bogenoemde toedienings op die fisiologie van die plante ondersoek deur die konsentrasies, opname tempo’s, en groei ekonomie van die plante vir stikstof (N), fosfaat (P) en kalium (K) te bepaal. Ons het gevind dat die groei van koring deur die toediening van houtskool bevorder is en dit blyk dat dié effek weens die teenwoordigheid van hoë K vlakke in die plantweefsel is. Die tweede doel van ons studie was om ‘n gis vanuit die risosfeer van ‘n monokotiel wat aan die familie Poacea behoort, naamlik Themeda triandra Forssk. (rooigras) te isoleer. Die vermoë van die isolaat om die groei van koring te bevorder was daarna getoets. Drie verskillende Cryptococcus spesies was vanuit die risosfeer van rooigras geïsoleer, nl. Cryptococcus zeae, Cryptococcus luteolus en Cryptococcus rajasthanensis. Omdat C. zeae in ‘n vorige studie vanaf mielies geisoleer was, is ‘n isolaat van hierdie spesie gebruik in verdere eksperimente. Met die doel om te bepaal of dié gisspesie koringgroei kan bevorder, was die effek van C. zeae op die ontkieming van koring bestudeer en vergelyk met dié van twee ander grond giste, nl. Cryptococcus podzolicus CAB 978 en Rhodotorula mucilaginosa CAB 826. Hierdie drie giste is ook ondersoek om die groei van koring in ‘n glashuis te bevorder. Na een en twee maande se groei was die getalle van giste teenwoordig in die risosfeer en grond verder weg van die wortels bepaal. Die effek van dié giste op die groei van koring is bepaal in terme van droë gewig asook die relatiewe wortel en halm groei tempos. Veranderinge in die nutrient status van koring is ondersoek deur die konsentrasies, groei-ekonomie en tempo van opname vir P, K, sink (Zn) en yster (Fe) te bepaal. Ons het gedurende dié studie gevind dat C. zeae CAB 1119 en C. podzolicus CAB 978 die ontkieming van koring kon verbeter. Ons het ook gevind dat C. zeae CAB 1119 die groei van koring gedurende die eerste en tweede maand van groei kon bevorder, terwyl C. podzolicus CAB 978 dit net gedurende die eerste maand kon vermag en R. mucilaginosa CAB 826 geen effek gehad het nie. Die verbeterde groei kon aan C. zeae CAB 1119, wat die P, K, Zn en Fe groei effektiwiteit van die plante verbeter het, toegeskryf word. Die verbetering van groei effektiwiteit het ‘n positiewe invloed op die relatiewe groeisnelheid van die wortels en halms gehad, en dus op koringgroei. Die laaste doel van die studie was om te bepaal of C. zeae CAB 1119 die groei van koring kon bevorder wanneer die koring in sand wat natuurlike mikrobiese populasies bevat en met houtskool aangevul is, gekweek word. Plante is met lewensvatbare of nielewensvatbare selle van C. zeae CAB 1119 behandel en gekweek in sanderige grond, en/of grond waarby 10% (w/w) houtskool toegevoeg is. Die plante is na een maand geoes en die groei bepaal in terme van droë massa en die relatiewe wortel en halm groei tempos. Die konsentrasies van P, K, Zn en Fe in die plante, asook die fisiologie van die plante, nl. groei ekonomie en tempo van opname, met betrekking tot P, K, Zn en Fe is bepaal, Ons het gevind dat plante wat in die houtskool-grond mengsel gekweek is en met lewensvatbare selle van C. zeae CAB 1119 behandel is die beste groei getoon het. Die verbeterde relatiewe groei tempos van die wortels en halms was mees waarskynlik die gevolg van verhoogde P en K konsentrasies in die plante. Hierdie studie toon nuwe resultate in verband met die gebruik van biologiese alternatiewes tot kunsmis.

Trichoderma species are soil-borne filamentous fungi widely utilized for their many plant health benefits, such as conferring improved growth, disease resistance and abiotic stress tolerance to their hosts. Many Trichoderma species are able to produce the auxin phytohormone indole-3-acetic acid (IAA), and its production has been suggested to promote root growth. Here we show that the production of IAA is strain dependent and diverse external stimuli are associated with its production. In in vitro assays, Arabidopsis primary root length was negatively affected by the interaction with some Trichoderma strains. In soil experiments, a continuum effect on plant growth was shown and this was also strain dependent. In plate assays, some strains of Trichoderma spp. inhibited the expression of the auxin reporter gene DR5 in Arabidopsis primary roots but not secondary roots. When Trichoderma spp. and A. thaliana were physically separated, enhancement of both shoot and root biomass, increased root production and chlorophyll content were observed, which strongly suggested that volatile production by the fungus influenced the parameters analyzed. Trichoderma strains T. virens Gv29.8, T. atroviride IMI206040, T. sp. "atroviride B" LU132, and T. asperellum LU1370 were demonstrated to promote plant growth through volatile production. However, contrasting differences were observed with LU1370 which had a negative effect on plant growth in soil but a positive effect in plate assays. Altogether our results suggest that the mechanisms and molecules involved in plant growth promotion by Trichoderma spp. are multivariable and are affected by the environmental conditions.

Plants naturally host complex microbial communities in which the plant and the symbiotic partners act as an integrated metaorganism. These communities include beneficial (i.e. plant growth promoting, PGP) microorganisms which provide fundamental ecological services able to enhance host plant fitness and stress tolerance. PGP microorganisms represent a potential bioresource for agricultural applications, especially for desert farming under the harsh environmental conditions occurring in hot/arid regions (i.e. drought and salinity). In this context, understanding the ecological aspects of the associated microorganisms is crucial to take advantage of their ecological services. Here, hot/desert ecosystems were selected and two contrasting plant categories were used as models: (i) wild plants (i.e. speargrasses) growing in hot-desert sand dunes and (ii) the main crop cultivated in desert ecosystems, the date palm. By using highthroughput DNA sequencing and microscopy, the ecology and functionality of the microbial communities associated with these plants were characterized. Additionally, the PGP services of bacteria isolated from date palm were explored. I found that the harsh conditions of the desert strongly affect the selection and assembly of microbial communities associated with three different speargrass species, determining a plant species-independent core microbiome always present among the three plant species and carrying important PGP traits. On the contrary, in agroecosystems where desert farming practices are used, the plant species, i.e. date palm exerts a stronger selective pressure than the environmental and edaphic factors favoring the recruitment of conserved microbial assemblages, independent of the differences in the soil and environmental conditions among the studied oases. Such selective pressure also favors the recruitment of conserved PGP microorganisms (i.e. Pseudomonas sp. bacterial strains) able to protect their host from salinity stress through the induction of root architectural changes regulated by the modification of the root system auxin homeostasis. Overall, we found that deserts are unique ecosystems that challenge the paradigm of microbial community assembly, as it was defined from studies in non-arid ecosystems. The understanding of the ecological features regulating the ecological properties of such unique microbial community assembly will be a key-step to improve the chances of successful application of ‘PGP microorganisms’ in arid agroecosystems.