Salinization of soil with sodium chloride ions inhibits plant functions, causing reduction of yield of crops. Salt tolerant microorganisms have been studied to enhance crop growth under salinity. This review describes the performance of endophytic fungi applied to crops as a supplement to plant genetics or soil management to alleviate salt stress in crops. This is achieved via inducing systemic resistance, increasing the levels of beneficial metabolites, activating antioxidant systems to scavenge ROS, and modulating plant growth phytohormones. Colonization by endophytic fungi improves nutrient uptake and maintains ionic homeostasis by modulating ion accumulation, thereby restricting the transport of Na + to leaves and ensuring a low cytosolic Na + :K + ratio in plants. Participating endophytic fungi enhance transcripts of genes encoding the high Affinity Potassium Transporter 1 (HKT1) and the inwardrectifying K + channels KAT1 and KAT2, which play key roles in regulating Na + and K + homeostasis. Endophytic-induced interplay of strigolactones play regulatory roles in salt tolerance by interacting with phytohormones. Future research requires further attention on the biochemical, molecular and genetic mechanisms crucial for salt stress resistance requires further attention for future research. Furthermore, to design strategies for sustained plant health with endophytic fungi, a new wave of exploration of plant-endophyte responses to combinations of stresses is mandatory.

A non-invasive plant phenotyping platform, GrowScreen-PaGe, was used to resolve the dynamics of shoot and root growth of the model cereal Brachypodium (Brachypodium distachyon Bd21-3) in response to the plant growth promoting (PGP) bacteria Azospirillum (Azospirillum brasilense Sp245). Inoculated Brachypodium plants had greater early vigor and higher P use efficiency than non-inoculated Brachypodium at low P and low temperature conditions. Root systems were imaged non-invasively at eight time points and data combined with leaf area, shoot biomass and nutrient content from destructive subsamples at 7, 14 and 21 days after inoculation (DAI). Azospirillum colonisation of roots improved Brachypodium shoot and, to a greater degree, root growth in three independent experiments. Inoculation promoted P use efficiency in shoots but not P concentration or uptake, despite increased total root length. Longer roots in inoculated plants arose from twofold faster branch root growth but slower axile root growth, detected at 11 DAI. Analysis of the spatio-temporal phenotypes indicated that the effects of Azospirillum inoculation increased as shoot P concentration declined, but the magnitude depended on the time after inoculation and growth rate of branch roots compared to axile roots. High throughput plant phenotyping platforms allow the details of plant-microorganism symbioses to be resolved, offering insights into the timing of changes in different tissues to allow molecular mechanisms to be determined.

Plant growth-promoting rhizobacteria (PGPR) are known to improve plant performance by multiple mechanisms, such as the production of beneficial hormones, the enhancement of plant nutritional status, and the reduction of the stress-related damage. The interaction between plants and PGPR becomes of particular interest in environments that are characterized by suboptimal growing conditions, e.g., high or low temperatures, drought, soil salinity, and nutrient scarcity. The positive role of PGPR will become even more appealing in the future, as world agriculture is facing issues as climate change and soil degradation. This chapter aims to discuss the main mechanisms of the interaction between PGPR and plants and will focus of how PGPR can decrease abiotic stress damage in cereals, which are critical crops for human diet.

In natural environments, interaction between plant roots and microorganisms are common. These interactions between microbial species and plants inhabited by them are being studied using various techniques. Metabolomics research based on mass spectrometric techniques is one of the crucial approaches that underpins system biology and relies on precision instrument analysis. In the last decade, this emerging field has received extensive attention. It provides a qualitative and quantitative approach for determining the mechanisms of symbiosis of bacteria and fungi with plants and also helps to elucidate the tolerance mechanisms of host plants against various abiotic stresses. However, this -omics application and its tools in plant–microbe interaction studies is still underutilized compared with genomic and transcriptomic methods. Therefore, it is crucial to bring this field forward to bear on the study of plant resistance and susceptibility. This review describes the current status of methods and progress in metabolomics applications for plant–microbe interaction studies discussing current challenges and future prospects.

The potential of plant growth promoting (PGP) bacteria in improving the performance of plants in suboptimal environments is increasingly acknowledged, but little information is available on the mechanisms underlying this interaction, particularly when plants are subjected to a combination of stresses. In this study, we investigated the effects of the inoculation with the PGP bacteria Azospirillum brasilense (Azospirillum) on the metabolism of the model cereal Brachypodium distachyon (Brachypodium) grown at low temperatures and supplied with insufficient phosphorus. Investigating polar metabolite and lipid fluctuations during early plant development, we found that the bacteria initially elicited a defense response in Brachypodium roots, while at later stages Azospirillum reduced the stress caused by phosphorus deficiency and improved root development of inoculated plants, particularly by stimulating the growth of branch roots. We propose that the interaction of the plant with Azospirillum was influenced by its nutritional status: bacteria were sensed as pathogens while plants were still phosphorus sufficient, but the interaction became increasingly beneficial for the plants as their phosphorus levels decreased. Our results provide new insights on the dynamics of the cereal-PGP bacteria interaction, and contribute to our understanding of the role of beneficial microorganisms in the growth of cereal crops in suboptimal environments.

As agriculture and food security face unprecedented challenges, emerging agricultural innovations and existing practices require ongoing examination in the context of sustainability. In this review, we focus on the use of probiotic microorganisms for improved plant production. As plants are enormously diverse, emphasis is placed on the fundamental sites of plant-microbe interactions regarding benefits and challenges encountered when altering the microbiome of these locations. The soil, the external plant epidermis, and internal plant tissue are considered in discussion regarding the type of plant probiotic application. Plant probiotics range from broader soil beneficial microorganisms (such as Trichoderma spp.) through to specialised epiphytes and endophytes (such as root nodule bacteria). As each site of interaction affects plant growth differently, potential outcomes from the introduction of these exogenous microorganisms are discussed with regard to plant productivity. Finally, recommendations regarding regulation and future use of plant probiotics are points of consideration throughout this review.

Plant growth promoting (PGP) bacteria are known to enhance plant growth and protect them from environmental stresses through different pathways. The rhizosphere of perennial plants, including olive, may represent a relevant reservoir of PGP bacteria. Here, seven bacterial strains isolated from olive rhizosphere have been characterized taxonomically by 16S sequencing and biochemically, to evaluate their PGP potential. Most strains were identified as Pseudomonas or Bacillus spp., while the most promising ones belonged to genera Pseudomonas and Curtobacterium. Those strains have been tested for their capacity to grow under osmotic or salinity stress and to improve the germination and early development of Triticum durum subjected or not to those stresses. The selected strains had the ability to grow under severe stress, and a positive effect has been observed in non-stressed seedlings inoculated with one of the Pseudomonas strains, which showed promising characteristics that should be further evaluated. The biochemical and taxonomical characterization of bacterial strains isolated from different niches and the evaluation of their interaction with plants under varying conditions will help to increase our knowledge on PGP microorganisms and their use in agriculture.

<p>The use of microorganisms for improving plant performance under limiting conditions can be traced throughout history. Interestingly the first commercial biological plant growth promotor was patented in 1896. However, the understanding how the organisms interact on molecular level really took off after the advent of the genomic era which produced the tools needed for understanding how plants and microorganisms modulate each-other’s gene expression and metabolism. Today more than ever, the holistic understanding of plant nutrient uptake and novel strategies to improve nutrient uptake are of utmost importance. Our work focuses on nitrogen (N) – the second most abundant nutrient in plants and phosphorus (P) – a finite global resource. We present studies where use of plant growth promoting rhizobacteria (PGPR) resulted in improved plant performance under limited N or P in Brachypodium - a model plant for cereals. Plant roots were analyzed with the non-invasive root phenotyping platform GrowScreen Page [1], or with the 3D printed EcoFab microcosms [2]. The latter was adapted and used in combination with Plant Screen Mobile [3], for non-invasive shoot area estimation, in conjunction with root scanning, over time. On the other hand, the performance of barley plants under the influence of 2 fungal interaction partners were investigated in soil system, using magnetic resonance imaging [4].</p><p>The plant response to a micro-organism is largely dependent on the surrounding conditions. Examples of plants treated with plant growth promoting rhizobacteria (PGPR) and grown under high and low N show that: the plant phenotype, N content within the plant and molecular response vary depending on the N availability in the surrounding medium.</p><p>Furthermore, we were able to dissect the plant phenotype of plants grown under limiting P in soil-less medium, and found that plant biomass was higher in plants inoculated with PGPR. A time series image-analysis of root phenotype showed the changes in root architecture, pin-pointing the time-window when growth promotion took effect after inoculation. A sand experiment confirmed these results.</p><p>Finally, the interaction between Barley roots and two fungi (a pathogen and a putative beneficial partner) was investigated to find dynamic response in root growth in soil that varied in soil depth, and had a different progression through time based on treatment.</p><p>We argue that for successful use of PGPR in context of nutrient uptake we need to account for: time in context of plant developmental stage [5] and moment of application, the organisms in question and the surrounding condition. Efforts are needed to elucidate the proper interaction partners and application points to result in a sustainable solution for agriculture.</p><ol><li>Funct Plant Biol, 2017. 44(1)</li> <li>New Phytol. 2019; 222(2): 1149–1160</li> <li>Plant Methods 2019 <strong>15:</strong>2</li> <li>Plant Physiol 170(3): 1176-1188.</li> <li>New Phytol. 2019 doi: 10.1111/nph.15955</li> </ol>