Dual RNA-seq transcriptional analysis of wheat roots colonized by Azospirillum brasilense reveals up-regulation of nutrient acquisition and cell cycle genes

Role of Plant-Growth-Promoting Rhizobacteria in Plant Machinery for Soil Heavy Metal Detoxification

Heavy metals migrate easily and are difficult to degrade in the soil environment, which causes serious harm to the ecological environment and human health. Thus, soil heavy metal pollution has become one of the main environmental issues of global concern. Plant-growth-promoting rhizobacteria (PGPR) is a kind of microorganism that grows around the rhizosphere and can promote plant growth and increase crop yield. PGPR can change the bioavailability of heavy metals in the rhizosphere microenvironment, increase heavy metal uptake by phytoremediation plants, and enhance the phytoremediation efficiency of heavy-metal-contaminated soils. In recent years, the number of studies on the phytoremediation efficiency of heavy-metal-contaminated soil enhanced by PGPR has increased rapidly. This paper systematically reviews the mechanisms of PGPR that promote plant growth (including nitrogen fixation, phosphorus solubilization, potassium solubilization, iron solubilization, and plant hormone secretion) and the mechanisms of PGPR that enhance plant-heavy metal interactions (including chelation, the induction of systemic resistance, and the improvement of bioavailability). Future research on PGPR should address the challenges in heavy metal removal by PGPR-assisted phytoremediation.

Transcriptional alterations of peanut root during interaction with growth-promoting Tsukamurella tyrosinosolvens strain P9

The plant growth-promoting rhizobacterium Tsukamurella tyrosinosolvens P9 can improve peanut growth. In this study, a co-culture system of strain P9 and peanut was established to analyze the transcriptome of peanut roots interacting with P9 for 24 and 72 h. During the early stage of co-culturing, genes related to mitogen-activated protein kinase (MAPK) and Ca2+ signal transduction, ethylene synthesis, and cell wall pectin degradation were induced, and the up-regulation of phenylpropanoid derivative, flavonoid, and isoflavone synthesis enhanced the defense response of peanut. The enhanced expression of genes associated with photosynthesis and carbon fixation, circadian rhythm regulation, indoleacetic acid (IAA) synthesis, and cytokinin decomposition promoted root growth and development. At the late stage of co-culturing, ethylene synthesis was reduced, whereas Ca2+ signal transduction, isoquinoline alkaloid synthesis, and ascorbate and aldarate metabolism were up-regulated, thereby maintaining root ROS homeostasis. Sugar decomposition and oxidative phosphorylation and nitrogen and fatty acid metabolism were induced, and peanut growth was significantly promoted. Finally, the gene expression of seedlings inoculated with strain P9 exhibited temporal differences. The results of our study, which explored transcriptional alterations of peanut root during interacting with P9, provide a basis for elucidating the growth-promoting mechanism of this bacterial strain in peanut.

Characterization and genomic insight of surfactin-producing Bacillus velezensis and its biocontrol potential against pathogenic contamination in lettuce hydroponics

Due to food borne pathogen, maintaining the viability of fresh fruits and vegetable is a great concern. Several strategies including microbial and plant-based formulations to reduce their infection and maintain quality of the fresh food are in practice. Currently, Bacillus has gained significant traction as a biocontrol agent for regulating diseases affecting a variety of agricultural and horticultural crops. Food-grade citric acid and plant growth-promoting rhizobacteria (PGPR) were used as antimicrobial agent, MIC results showed that PGPR (14.87 mm) and CA (20.25 mm) exhibited notable antimicrobial activity against E. coli. Lettuce treated with PGPR showed reduction in E. coli contamination, E. coli was detected at 3.30, 3.68 in control, and 2.7 log CFU/g in random root injury lettuce inoculated with PGPR KACC 21110 respectively. Random root injury showed a trend toward increasing E. coli internalization. The strains exhibited resistance to multiple antibiotics, including Imipenem, tetracycline, ampicillin, cefotaxime, cefoxitin, and ceftriaxone. Comprehensive data analysis revealed the presence of ten putative bacteriocin or bacteriocin-like gene clusters. The structure of lipopeptide homologs was characterized by using QTOF-MS/MS. The mass ion peaks attributed to surfactin homologs, surfactin A ion at m/z 1008.66, surfactin B, C at m/z 1022.67 and 1036.69. In addition to surfactin, a polyketide oxydifficidin and lipopeptide NO were extracted and detected from the extract of B. velezensis. Both isolates are key biocontrol agents and have significant potential in combating foodborne pathogens and can be utilized to explore novel antibacterial products for preventing pathogens in fresh produce.

Azospirillum brasilense improves rice growth under salt stress by regulating the expression of key genes involved in salt stress response, abscisic acid signaling, and nutrient transport, among others

Major food crops, such as rice and maize, display severe yield losses (30-50%) under salt stress. Furthermore, problems associated with soil salinity are anticipated to worsen due to climate change. Therefore, it is necessary to implement sustainable agricultural strategies, such as exploiting beneficial plant-microbe associations, for increased crop yields. Plants can develop associations with beneficial microbes, including arbuscular mycorrhiza and plant growth-promoting bacteria (PGPB). PGPB improve plant growth via multiple mechanisms, including protection against biotic and abiotic stresses. Azospirillum brasilense, one of the most studied PGPB, can mitigate salt stress in different crops. However, little is known about the molecular mechanisms by which A. brasilense mitigates salt stress. This study shows that total and root plant mass is improved in A. brasilense-inoculated rice plants compared to the uninoculated plants grown under high salt concentrations (100 mM and 200 mM NaCl). We observed this growth improvement at seven- and fourteen days post-treatment (dpt). Next, we used transcriptomic approaches and identified differentially expressed genes (DEGs) in rice roots when exposed to three treatments: 1) A. brasilense, 2) salt (200 mM NaCl), and 3) A. brasilense and salt (200 mM NaCl), at seven dpt. We identified 786 DEGs in the A. brasilense-treated plants, 4061 DEGs in the salt-stressed plants, and 1387 DEGs in the salt-stressed A. brasilense-treated plants. In the A. brasilense-treated plants, we identified DEGs involved in defense, hormone, and nutrient transport, among others. In the salt-stressed plants, we identified DEGs involved in abscisic acid and jasmonic acid signaling, antioxidant enzymes, sodium and potassium transport, and calcium signaling, among others. In the salt-stressed A. brasilense-treated plants, we identified some genes involved in salt stress response and tolerance (e.g., abscisic acid and jasmonic acid signaling, antioxidant enzymes, calcium signaling), and sodium and potassium transport differentially expressed, among others. We also identified some A. brasilense-specific plant DEGs, such as nitrate transporters and defense genes. Furthermore, our results suggest genes involved in auxin and ethylene signaling are likely to play an important role during these interactions. Overall, our transcriptomic data indicate that A. brasilense improves rice growth under salt stress by regulating the expression of key genes involved in defense and stress response, abscisic acid and jasmonic acid signaling, and ion and nutrient transport, among others. Our findings will provide essential insights into salt stress mitigation in rice by A. brasilense.

Unlocking the hidden potential of Mexican teosinte seeds: revealing plant growth-promoting bacterial and fungal biocontrol agents

The bacterial component of plant holobiont maintains valuable interactions that contribute to plants' growth, adaptation, stress tolerance, and antagonism to some phytopathogens. Teosinte is the grass plant recognized as the progenitor of modern maize, domesticated by pre-Hispanic civilizations around 9,000 years ago. Three teosinte species are recognized: Zea diploperennis, Zea perennis, and Zea mays. In this work, the bacterial diversity of three species of Mexican teosinte seeds was explored by massive sequencing of 16S rRNA amplicons. Streptomyces, Acinetobacter, Olivibacter, Erwinia, Bacillus, Pseudomonas, Cellvibrio, Achromobacter, Devosia, Lysobacter, Sphingopyxis, Stenotrophomonas, Ochrobactrum, Delftia, Lactobacillus, among others, were the bacterial genera mainly represented. The bacterial alpha diversity in the seeds of Z. diploperennis was the highest, while the alpha diversity in Z. mays subsp. mexicana race was the lowest observed among the species and races. The Mexican teosintes analyzed had a core bacteriome of 38 bacterial genera, including several recognized plant growth promoters or fungal biocontrol agents such as Agrobacterium, Burkholderia, Erwinia, Lactobacillus, Ochrobactrum, Paenibacillus, Pseudomonas, Sphingomonas, Streptomyces, among other. Metabolic inference analysis by PICRUSt2 of bacterial genera showed several pathways related to plant growth promotion (PGP), biological control, and environmental adaptation. The implications of these findings are far-reaching, as they highlight the existence of an exceptional bacterial germplasm reservoir teeming with potential plant growth promotion bacteria (PGPB). This reserve holds the key to cultivating innovative bioinoculants and formidable fungal antagonistic strains, thereby paving the way for a more sustainable and eco-friendly approach to agriculture. Embracing these novel NGS-based techniques and understanding the profound impact of the vertical transference of microorganisms from seeds could revolutionize the future of agriculture and develop a new era of symbiotic harmony between plants and microbes.

Plant growth-promoting rhizobacteria: A good companion for heavy metal phytoremediation

Phytoremediation is an environment-friendly approach regarded as a potential candidate for remediating heavy metal (HM)-contaminated soils. However, the low efficacy of phytoremediation is a major limitation that hampers its large-scale application. Therefore, developing strategies to enhance phytoremediation efficacy for contaminated soils is crucial. Plant growth-promoting rhizobacteria (PGPR) considerably contribute to phytoremediation intensification. To improve the efficiency of plant-microbe symbiosis for remediation, the mechanisms underlying PGPR-stimulated HM accumulation and tolerance in plants should be comprehensively understood. This review focuses on hyperaccumulators, PGPR, and the mechanisms by which PGPR enhance phytoremediation from four aspects: providing nutrients to plants, secreting plant hormones and specific enzymes, inducing systemic resistance, and altering the bioavailability of HMs in soils. It also provides a theoretical and technical basis for future research on PGPR synergism in promoting the phytoextraction efficiency in HM-contaminated soils.

Endophytes Modulate Plant Genes: Present Status and Future Perspectives

Interactions among endophytes and plants are widespread and can vary from neutral or positive or negative. Plants are continually in a functionally dynamic state due to interactions with diverse endophytic microorganisms, which produce various metabolic substances. Through quorum sensing, these substances not only help endophytes to outcompete other host-associated pathogens or microbes but also allow them to overcome the plant immune system. Manifold interactions between endophytic microbiota cause a reflective impact on the host plant functioning and the development of 'endobiomes,' by synthesizing chemicals that fill the gap between host and endophytes. Despite the advances in the field, specific mechanisms for the endophytes' precise methods to modulate plant genome and their effects on host plants remain poorly understood. Deeper genomic exploration can provide a locked away understanding of the competencies of endophytes and their conceivable function in host growth and health. Endophytes also can modify host metabolites, which could manipulate plants' growth, adaptation, and proliferation, and can be a more exciting and puzzling topic that must be properly investigated. The consequence of the interaction of endophytes on the host genome was analyzed as it can help unravel the gray areas of endophytes about which very little or no knowledge exists. This review discusses the recent advances in understanding the future challenges in the emerging research investigating how endosymbionts affect the host's metabolism and gene expression as an effective strategy for imparting resistance to biotic and abiotic challenges.

Large effect of phosphate-solubilizing bacteria on the growth and gene expression of Salix spp. at low phosphorus levels

Phosphorus is one of the most important nutrients required for plant growth and development. However, owing to its low availability in the soil, phosphorus is also one of the most difficult elements for plants to acquire. Phosphorus released into the soil from bedrock quickly becomes unavailable to plants, forming poorly soluble complexes. Phosphate-solubilizing bacteria (PSB) can solubilize unavailable phosphorus-containing compounds into forms in which phosphorus is readily available, thus promoting plant growth. In this study, two willow species, Salix dasyclados cv. Loden and Salix schwerinii × Salix viminalis cv. Tora, were inoculated with two selected bacterial strains, Pantoea agglomerans and Paenibacillus spp., to evaluate the plant growth parameters and changes in gene expression in the presence of different concentrations of tricalcium phosphate: 0 mM (NP), 1 mM (LP), and 2 mM (HP). Inoculation with PSB increased root, shoot and leaf biomass, and for the HP treatment, significant changes in growth patterns were observed. However, the growth responses to plant treatments tested depended on the willow species. Analysis of the leaf transcriptomes of the phosphate-solubilizing bacterium-inoculated plants showed a large variation in gene expression between the two willow species. For the Tora willow species, upregulation of genes was observed, particularly for those involved in pathways related to photosynthesis, and this effect was strongly influenced by bacterial phosphate solubilization. The Loden willow species was characterized by a general downregulation of genes involved in pathway activity that included ion transport, transcription regulation and chromosomes. The results obtained in this study provide an improved understanding of the dynamics of Salix growth and gene expression under the influence of PSB, contributing to an increase in yield and phosphorus-use efficiency.

The Biosynthesis and Functions of Polyamines in the Interaction of Plant Growth-Promoting Rhizobacteria with Plants

Plant growth-promoting rhizobacteria (PGPR) are members of the plant rhizomicrobiome that enhance plant growth and stress resistance by increasing nutrient availability to the plant, producing phytohormones or other secondary metabolites, stimulating plant defense responses against abiotic stresses and pathogens, or fixing nitrogen. The use of PGPR to increase crop yield with minimal environmental impact is a sustainable and readily applicable replacement for a portion of chemical fertilizer and pesticides required for the growth of high-yielding varieties. Increased plant health and productivity have long been gained by applying PGPR as commercial inoculants to crops, although with uneven results. The establishment of plant-PGPR relationships requires the exchange of chemical signals and nutrients between the partners, and polyamines (PAs) are an important class of compounds that act as physiological effectors and signal molecules in plant-microbe interactions. In this review, we focus on the role of PAs in interactions between PGPR and plants. We describe the basic ecology of PGPR and the production and function of PAs in them and the plants with which they interact. We examine the metabolism and the roles of PAs in PGPR and plants individually and during their interaction with one another. Lastly, we describe some directions for future research.

Ovarian transcriptional response to Wolbachia infection in D. melanogaster in the context of between-genotype variation in gene expression

Wolbachia is a maternally transmitted endosymbiotic bacteria that infects a wide variety of arthropod and nematode hosts. The effects of Wolbachia on host biology are far-reaching and include changes in host gene expression. However, previous work on the host transcriptional response has generally been investigated in the context of a single host genotype. Thus, the relative effect of Wolbachia infection versus vs. host genotype on gene expression is unknown. Here, we explicitly test the relative roles of Wolbachia infection and host genotype on host gene expression by comparing the ovarian transcriptomes of 4 strains of Drosophila melanogaster (D. melanogaster) infected and uninfected with Wolbachia. Our data suggest that infection explains a small amount of transcriptional variation, particularly in comparison to variation in gene expression among strains. However, infection specifically affects genes related to cell cycle, translation, and metabolism. We also find enrichment of cell division and recombination processes among genes with infection-associated differential expression. Broadly, the transcriptomic changes identified in this study provide novel understanding of the relative magnitude of the effect of Wolbachia infection on gene expression in the context of host genetic variation and also point to genes that are consistently differentially expressed in response to infection among multiple genotypes.

Transcriptional landscape of Brachypodium distachyon roots during interaction with Bacillus velezensis strain B26

Plant growth promoting rhizobacteria (PGPR) communicate with plants through roots. The molecular mechanism by which plants and PGPR respond to each other is not very well known. In the current study, we did RNA sequence analysis of Brachypodium distachyon Bd21-3 roots inoculated with PGPR, Bacillus velezensis strain B26. From our list of differentially expressed genes, we concentrated on transcripts that have a high possibility of participating in plant-PGPR interaction. Transcripts associated to the hormone signalling pathway were differentially expressed. We identified the upregulation of various transcripts linked to ion transporters. Reduction in expression of defense signalling genes indicated that B26 suppresses the plant defense mechanisms to begin successful interaction with roots. Transcripts associated with lignin branch of the phenylpropanoid pathway were upregulated as well, leading to more accumulation of lignin in the cell wall which enhances mechanical strength of plants. Overall, this study is an excellent resource for investigating associations between plant-PGPR interactions.

Transcriptome Landscapes of Salt-Susceptible Rice Cultivar IR29 Associated with a Plant Growth Promoting Endophytic Streptomyces

Plant growth-promoting endophytic (PGPE) actinomycetes have been known to enhance plant growth and mitigate plant from abiotic stresses via their PGP-traits. In this study, PGPE Streptomyces sp. GKU 895 promoted growth and alleviated salt tolerance of salt-susceptible rice cultivar IR29 by augmentation of plant weight and declined ROS after irrigation with 150 mM NaCl in a pot experiment. Transcriptome analysis of IR29 exposed to the combination of strain GKU 895 and salinity demonstrated up and downregulated differentially expressed genes (DEGs) classified by gene ontology and plant reactome. Streptomyces sp. GKU 895 induced changes in expression of rice genes including transcription factors under salt treatment which involved in growth and development, photosynthesis, plant hormones, ROS scavenging, ion transport and homeostasis, and plant-microbe interactions regarding pathogenesis- and symbiosis-related proteins. Taken together, these data demonstrate that PGPE Streptomyces sp. GKU 895 colonized and enhanced growth of rice IR29 and triggered salt tolerance phenotype. Our findings suggest that utilisation of beneficial endophytes in the saline fields could allow for the use of such marginal soils for growing rice and possibly other crops.

Biocontrol and plant growth promotion by combined Bacillus spp. inoculation affecting pathogen and AMF communities in the wheat rhizosphere at low salt stress conditions

Applying plant growth-promoting rhizobacteria (PGPR) improves the efficiency of soil-borne disease control and is considered a sustainable practice. However, the effect of PGPR on the fungal community, especially pathogenic fungi and arbuscular mycorrhizal fungi (AMF), remains unclear. In this study, we examined the effects of a compound microbial agent (consisting of Bacillus subtilis HG-15 and Bacillus velezensis JC-K3) on the incidence and yield of wheat under low salt stress, as well as compared the diversity and community composition of the rhizosphere fungal and AMF communities of wheat in the CK (not inoculated bacterial agent) and BIO (inoculated with a bacterial agent) groups. Chlorophyll relative content (SPAD), net photosynthesis rate (Pn), transpiration rate (Tr), leaf water use efficiency (WUE _L), grains per spike and wheat yield in the BIO group increased more than in the CK group. The number of diseased plants and disease incidence was observed to be reduced. The relative efficacy reached 79.80%. We classified 1007 fungal operational taxonomic units (OTU) based on Miseq sequencing data: 11 phyla, 173 families, 319 genera, and 521 species. Fifty-four OTUs were classified from the AMF effective sequences, including 1 phylum, 3 families, 3 genera, and 17 species. The inoculation of bacterial agents reduced the relative abundance of pathogen genera such as Gibberella, Fusarium, Cladosporium, and Alternaria in wheat rhizosphere. It increased the relative abundance of AMF species such as Glomus-group-B-Glomus-lamellosu-VTX00193, Glomus-viscosum-VTX00063, and Glomus-Glo2-VTX00280. In addition, pH, EC, exchangeable K, available N, total N, organic matter, and olsen P were the main driving forces for shaping wheat rhizosphere fungi. The pH value was positively correlated with the relative abundance of fungal communities in soil, especially Gibberella, Cladosporium, Fusarium, and Alternaria. In summary, inoculation with Bacillus subtilis HG-15 and Bacillus velezensis JC-K3 affected wheat yield, incidence, rhizosphere soil chemical properties, rhizosphere fungi, and AMF fungal diversity and community. The findings may provide a theoretical foundation and strain support for constructing efficient PGPR-community and clarifying its mechanism of pathogenic bacteria inhibition.

Endophytes and their potential in biotic stress management and crop production

Biotic stress is caused by harmful microbes that prevent plants from growing normally and also having numerous negative effects on agriculture crops globally. Many biotic factors such as bacteria, fungi, virus, weeds, insects, and nematodes are the major constrains of stress that tends to increase the reactive oxygen species that affect the physiological and molecular functioning of plants and also led to the decrease in crop productivity. Bacterial and fungal endophytes are the solution to overcome the tasks faced with conventional farming, and these are environment friendly microbial commodities that colonize in plant tissues without causing any damage. Endophytes play an important role in host fitness, uptake of nutrients, synthesis of phytohormone and diminish the injury triggered by pathogens via antibiosis, production of lytic enzymes, secondary metabolites, and hormone activation. They are also reported to help plants in coping with biotic stress, improving crops and soil health, respectively. Therefore, usage of endophytes as biofertilizers and biocontrol agent have developed an eco-friendly substitute to destructive chemicals for plant development and also in mitigation of biotic stress. Thus, this review highlighted the potential role of endophytes as biofertilizers, biocontrol agent, and in mitigation of biotic stress for maintenance of plant development and soil health for sustainable agriculture.

The Impact of Non-Nodulating Diazotrophic Bacteria in Agriculture: Understanding the Molecular Mechanisms That Benefit Crops

Agriculture is facing increasing challenges with regard to achieving sustainable growth in productivity without negatively impacting the environment. The use of bioinoculants is emerging as a sustainable solution for agriculture, especially bioinoculants based on diazotrophic bacteria. Brazil is at the forefront of studies intended to identify beneficial diazotrophic bacteria, as well as in the molecular characterization of this association on both the bacterial and plant sides. Here we highlight the main advances in molecular studies to understand the benefits brought to plants by diazotrophic bacteria. Different molecular pathways in plants are regulated both genetically and epigenetically, providing better plant performance. Among them, we discuss the involvement of genes related to nitrogen metabolism, cell wall formation, antioxidant metabolism, and regulation of phytohormones that can coordinate plant responses to environmental factors. Another important aspect in this regard is how the plant recognizes the microorganism as beneficial. A better understanding of plant–bacteria–environment interactions can assist in the future formulation of more efficient bioinoculants, which could in turn contribute to more sustainable agriculture practices.

Transcriptomic and metabonomic insights into the biocontrol mechanism of Trichoderma asperellum M45a against watermelon Fusarium wilt

Watermelon (Citrullus lanatus) is one of the most popular fruit crops. However, Fusarium wilt (FW) is a serious soil-borne disease caused by Fusarium oxysporum f. sp. niveum (FON) that severely limits the development of the watermelon industry. Trichoderma spp. is an important plant anti-pathogen biocontrol agent. The results of our previous study indicated that Trichoderma asperellum M45a (T. asperellum M45a) could control FW by enhancing the relative abundance of plant growth-promoting rhizobacteria (PGPR) in the rhizosphere of watermelon. However, there are few studies on its mechanism in the pathogen resistance of watermelon. Therefore, transcriptome sequencing of T. asperellum M45a-treated watermelon roots combined with metabolome sequencing of the rhizosphere soil was performed with greenhouse pot experiments. The results demonstrated that T. asperellum M45a could stably colonize roots and significantly increase the resistance-related enzymatic activities (e.g., lignin, cinnamic acid, peroxidase and peroxidase) of watermelon. Moreover, the expression of defense-related genes such as MYB and PAL in watermelon roots significantly improved with the inoculation of T. asperellum M45a. In addition, KEGG pathway analysis showed that a large number of differentially expressed genes were significantly enriched in phenylpropane metabolic pathways, which may be related to lignin and cinnamic acid synthesis, thus further inducing the immune response to resist FON. Furthermore, metabolic analysis indicated that four differential metabolic pathways were enriched in M45a-treated soil, including six upregulated compounds and one down-regulated compound. Among them, galactinol and urea were significantly positively correlated with Trichoderma. Hence, this study provides insight into the biocontrol mechanism of T. asperellum M45a to resist soil-borne diseases, which can guide its industrial application.

Integrative Analysis of Genes Involved in the Global Response to Potato Wart Formation

Synchytrium endobioticum, the causal agent of potato wart disease, poses a major threat to commercial potato production. Understanding the roles of transcriptionally regulated genes following pathogen infection is necessary for understanding the system-level host response to pathogen. Although some understanding of defense mechanisms against S. endobioticum infection has been gained for incompatible interactions, the genes and signaling pathways involved in the compatible interaction remain unclear. Based on the collection of wart diseased tubers of a susceptible cultivar, we performed phenotypic and dual RNA-Seq analyses of wart lesions in seven stages of disease progression. We totally detected 5,052 differentially expressed genes (DEGs) by comparing the different stages of infection to uninfected controls. The tendency toward differential gene expression was active rather than suppressed under attack by the pathogen. The number of DEGs step-up along with the development of the disease and the first, third and seventh of the disease stages showed substantially increase of DEGs in comparison of the previous stage. The important functional groups identified via Gene ontology (GO) and KEGG enrichment were those responsible for plant-pathogen interaction, fatty acid elongation and phenylpropanoid biosynthesis. Gene coexpression networks, composed of 17 distinct gene modules that contained between 25 and 813 genes, revealed high interconnectivity of the induced response and led to the identification of a number of hub genes enriched at different stages of infection. These results provide a comprehensive perspective on the global response of potato to S. endobioticum infection and identify a potential transcriptional regulatory network underlying this susceptible response, which contribute to a better understanding of the potato-S. endobioticum pathosystem.

Significance of the Diversification of Wheat Species for the Assembly and Functioning of the Root-Associated Microbiome

Wheat, one of the major crops in the world, has had a complex history that includes genomic hybridizations between Triticum and Aegilops species and several domestication events, which resulted in various wild and domesticated species (especially Triticum aestivum and Triticum durum), many of them still existing today. The large body of information available on wheat-microbe interactions, however, was mostly obtained without considering the importance of wheat evolutionary history and its consequences for wheat microbial ecology. This review addresses our current understanding of the microbiome of wheat root and rhizosphere in light of the information available on pre- and post-domestication wheat history, including differences between wild and domesticated wheats, ancient and modern types of cultivars as well as individual cultivars within a given wheat species. This analysis highlighted two major trends. First, most data deal with the taxonomic diversity rather than the microbial functioning of root-associated wheat microbiota, with so far a bias toward bacteria and mycorrhizal fungi that will progressively attenuate thanks to the inclusion of markers encompassing other micro-eukaryotes and archaea. Second, the comparison of wheat genotypes has mostly focused on the comparison of T. aestivum cultivars, sometimes with little consideration for their particular genetic and physiological traits. It is expected that the development of current sequencing technologies will enable to revisit the diversity of the wheat microbiome. This will provide a renewed opportunity to better understand the significance of wheat evolutionary history, and also to obtain the baseline information needed to develop microbiome-based breeding strategies for sustainable wheat farming.

PRGdb 4.0: an updated database dedicated to genes involved in plant disease resistance process

The Plant Resistance Genes database (PRGdb; http://prgdb.org/prgdb4/) has been greatly expanded, keeping pace with the increasing amount of available knowledge and data (sequenced proteomes, cloned genes, public analysis data, etc.). The easy-to-use style of the database website has been maintained, while an updated prediction tool, more data and a new section have been added. This new section will contain plant resistance transcriptomic experiments, providing additional easy-to-access experimental information. DRAGO3, the tool for automatic annotation and prediction of plant resistance genes behind PRGdb, has been improved in both accuracy and sensitivity, leading to more reliable predictions. PRGdb offers 199 reference resistance genes and 586.652 putative resistance genes from 182 sequenced proteomes. Compared to the previous release, PRGdb 4.0 has increased the number of reference resistance genes from 153 to 199, the number of putative resistance genes from 177K from 76 proteomes to 586K from 182 sequenced proteomes. A new section has been created that collects plant-pathogen transcriptomic data for five species of agricultural interest. Thereby, with these improvements and data expansions, PRGdb 4.0 aims to serve as a reference to the plant scientific community and breeders worldwide, helping to further study plant resistance mechanisms that contribute to fighting pathogens.

Coordinated bacterial and plant sulfur metabolism in Enterobacter sp. SA187-induced plant salt stress tolerance

Although plant growth–promoting bacteria (PGPB) enhance the performance of plants, only a few mechanisms have been identified so far. We show that the sulfur metabolisms in both PGPB Enterobacter sp. SA187 and Arabidopsis plants play a key role in plant salt stress tolerance. Salt stress induces a sulfur starvation response in plants that is attenuated by SA187. Arabidopsis sulfur metabolic mutants are hypersensitive to salt stress but can be rescued by SA187. Most plant sulfur metabolism occurs in chloroplasts and is linked to stress-induced accumulation of reactive oxygen species that is suppressed by SA187. This work reveals that plant salt stress tolerance requires the coordinated regulation of the sulfur metabolic pathways in both beneficial microbe and host plant.

Enterobacter sp. SA187 is a root endophytic bacterium that maintains growth and yield of plants under abiotic stress conditions. In this work, we compared the metabolic wirings of Arabidopsis and SA187 in the free-living and endophytic interaction states. The interaction of SA187 with Arabidopsis induced massive changes in bacterial gene expression for chemotaxis, flagellar biosynthesis, quorum sensing, and biofilm formation. Besides modification of the bacterial carbon and energy metabolism, various nutrient and metabolite transporters and the entire sulfur pathway were up-regulated. Under salt stress, Arabidopsis resembled plants under sulfate starvation but not when colonized by SA187, which reprogramed the sulfur regulon of Arabidopsis. In accordance, salt hypersensitivity of multiple Arabidopsis sulfur metabolism mutants was partially or completely rescued by SA187 as much as by the addition of sulfate, L-cysteine, or L-methionine. Many components of the sulfur metabolism that are localized in the chloroplast were partially rescued by SA187. Finally, salt-induced accumulation of reactive oxygen species as well as the hypersensitivity of LSU mutants were suppressed by SA187. LSUs encode a central regulator linking sulfur metabolism to chloroplast superoxide dismutase activity. The coordinated regulation of the sulfur metabolic pathways in both the beneficial microorganism and the host plant is required for salt stress tolerance in Arabidopsis and might be a common mechanism utilized by different beneficial microbes to mitigate the harmful effects of different abiotic stresses on plants.

Mixed Transcriptome Analysis Revealed the Possible Interaction Mechanisms between Zizania latifolia and Ustilago esculenta Inducing Jiaobai Stem-Gall Formation

The smut fungus Ustilago esculenta infects Zizania latifolia and induces stem expansion to form a unique vegetable named Jiaobai. Although previous studies have demonstrated that hormonal control is essential for triggering stem swelling, the role of hormones synthesized by Z. latifolia and U. esculenta and the underlying molecular mechanism are not yet clear. To study the mechanism that triggers swollen stem formation, we analyzed the gene expression pattern of both interacting organisms during the initial trigger of culm gall formation, at which time the infective hyphae also propagated extensively and penetrated host stem cells. Transcriptional analysis indicated that abundant genes involving fungal pathogenicity and plant resistance were reprogrammed to maintain the subtle balance between the parasite and host. In addition, the expression of genes involved in auxin biosynthesis of U. esculenta obviously decreased during stem swelling, while a large number of genes related to the synthesis, metabolism and signal transduction of hormones of the host plant were stimulated and showed specific expression patterns, particularly, the expression of ZlYUCCA9 (a flavin monooxygenase, the key enzyme in indole-3-acetic acid (IAA) biosynthesis pathway) increased significantly. Simultaneously, the content of IAA increased significantly, while the contents of cytokinin and gibberellin showed the opposite trend. We speculated that auxin produced by the host plant, rather than the fungus, triggers stem swelling. Furthermore, from the differently expressed genes, two candidate Cys2-His2 (C2H2) zinc finger proteins, GME3058_g and GME5963_g, were identified from U. esculenta, which may conduct fungus growth and infection at the initial stage of stem-gall formation.

Transcriptome Analyses of Barley Roots Inoculated with Novel Paenibacillus sp. and Erwinia gerundensis Strains Reveal Beneficial Early-Stage Plant-Bacteria Interactions

Plant growth-promoting bacteria can improve host plant traits including nutrient uptake and metabolism and tolerance to biotic and abiotic stresses. Understanding the molecular basis of plant–bacteria interactions using dual RNA-seq analyses provides key knowledge of both host and bacteria simultaneously, leading to future enhancements of beneficial interactions. In this study, dual RNA-seq analyses were performed to provide insights into the early-stage interactions between barley seedlings and three novel bacterial strains (two Paenibacillus sp. strains and one Erwinia gerundensis strain) isolated from the perennial ryegrass seed microbiome. Differentially expressed bacterial and barley genes/transcripts involved in plant–bacteria interactions were identified, with varying species- and strain-specific responses. Overall, transcriptome profiles suggested that all three strains improved stress response, signal transduction, and nutrient uptake and metabolism of barley seedlings. Results also suggested potential improvements in seedling root growth via repressing ethylene biosynthesis in roots. Bacterial secondary metabolite gene clusters producing compounds that are potentially associated with interactions with the barley endophytic microbiome and associated with stress tolerance of plants under nutrient limiting conditions were also identified. The results of this study provided the molecular basis of plant growth-promoting activities of three novel bacterial strains in barley, laid a solid foundation for the future development of these three bacterial strains as biofertilisers, and identified key differences between bacterial strains of the same species in their responses to plants.

Combined Use of Endophytic Bacteria and Pre-Sowing Treatment of Thiamine Mitigates the Adverse Effects of Drought Stress in Wheat (Triticum aestivum L.) Cultivars

On a global scale, wheat (Triticum aestivum L.) is a widely cultivated crop among all cereals. Increasing pollution, population expansion, socio-economic development, ecological and industrial policies have induced changes in overall climatic attributes. The impact of these factors on agriculture dynamics has led to various biotic and abiotic stresses, i.e., significant decline in rainfall, directly affect sustainable agriculture. Increasing abiotic stresses have a direct negative effect on worldwide crop production. More promising and improved stress-tolerant strategies that can help to feed the increasing global population are required. A laboratory experiment was performed on two of the latest wheat (Triticum aestivum L.) genotypes (Akbar 2019 and Anaj 2017) from Punjab Pakistan, to determine the influence of seed priming with thiamine (vitamin B1) along with soil inoculation of Endophytic bacterial strains to mitigate the effects of drought stress at different degrees. Results revealed that thiamine helped in the remote germination; seeds of Anaj 2017 germinated within 16 hours while Akbar 2019 germinated after one day. Overall growth parameters of Anaj 2017 were negatively affected even under higher levels of drought stress, while Akbar 2019 proved to be a susceptible cultivar. A significant increase in RFW (54%), SFW (85%), RDW (69%), SDW (67%) and TChl (136%) validated the effectiveness of D-T3 compared to C-T0 in drought stress. Significant decrease in MDA, EL and H2O2 signified the imperative function of D-T3 over C-T0 under drought stress. In conclusion and recommendation, we declare that farmers can get better wheat growth under drought stress by application of D-T3 over C-T0.

Characterization of glutamine synthetase from the ammonium-excreting strain HM053 of Azospirillum brasilense

Glutamine synthetase (GS), encoded by glnA, catalyzes the conversion of L-glutamate and ammonium to L-glutamine. This ATP hydrolysis driven process is the main nitrogen assimilation pathway in the nitrogen-fixing bacterium Azospirillum brasilense. The A. brasilense strain HM053 has poor GS activity and leaks ammonium into the medium under nitrogen fixing conditions. In this work, the glnA genes of the wild type and HM053 strains were cloned into pET28a, sequenced and overexpressed in E. coli. The GS enzyme was purified by affinity chromatography and characterized. The GS of HM053 strain carries a P347L substitution, which results in low enzyme activity and rendered the enzyme insensitive to adenylylation by the adenilyltransferase GlnE.

Herbaspirillum seropedicae strain HRC54 expression profile in response to sugarcane apoplastic fluid

Bacterial transcriptome profiling in the presence of plant fluids or extracts during microbial growth may provide relevant information on plant-bacteria interactions. Here, RNA sequencing (RNA-Seq) was used to determine the transcriptomic profile of Herbaspirillum seropedicae strain HRC54 at the early stages of response to sugarcane apoplastic fluid. Differentially expressed gene (DEG) analysis was performed using the DESeq2 and edgeR packages, followed by functional annotation using Blast2GO and gene ontology enrichment analysis using the COG and KEGG databases. After 2 h of sugarcane apoplastic fluid addition to the H. seropedicae HRC54 culture, respectively, 44 and 45 genes were upregulated and downregulated. These genes were enriched in bacterial metabolism (e.g., oxidoreductase and transferase), ABC transporters, motility, secretion systems, and signal transduction. RNA-Seq expression profiles of 12 genes identified in data analyses were verified by RT-qPCR. The results suggested that H. seropedicae HRC54 recognized sugarcane apoplastic fluid as the host signal, and some DEGs were closely involved at the early stages of the establishment of plant-bacteria interactions.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02848-y.

Redox Regulation in Diazotrophic Bacteria in Interaction with Plants

Plants interact with a large number of microorganisms that greatly influence their growth and health. Among the beneficial microorganisms, rhizosphere bacteria known as Plant Growth Promoting Bacteria increase plant fitness by producing compounds such as phytohormones or by carrying out symbioses that enhance nutrient acquisition. Nitrogen-fixing bacteria, either as endophytes or as endosymbionts, specifically improve the growth and development of plants by supplying them with nitrogen, a key macro-element. Survival and proliferation of these bacteria require their adaptation to the rhizosphere and host plant, which are particular ecological environments. This adaptation highly depends on bacteria response to the Reactive Oxygen Species (ROS), associated to abiotic stresses or produced by host plants, which determine the outcome of the plant-bacteria interaction. This paper reviews the different antioxidant defense mechanisms identified in diazotrophic bacteria, focusing on their involvement in coping with the changing conditions encountered during interaction with plant partners.

Microbiome for sustainable agriculture: a review with special reference to the corn production system

Microbial diversity formed by ages of evolution in soils plays an important role in sustainability of crop production by enriching soil and alleviating biotic and abiotic stresses. This diversity is as an essential part of the agro-ecosystems, which is being pushed to edges by pumping agrochemicals and constant soil disturbances. Consequently, efficiency of cropping system has been decreasing, aggravated further by the increased incidence of abiotic stresses due to changes in climatic patterns. Thus, the sustainability of agriculture is at stake. Understanding the microbiota inhabiting phyllosphere, endosphere, spermosphere, rhizosphere, and non-rhizosphere, and its utilization could be a sustainable crop production strategy. This review explores the available information on diversity of beneficial microbes in agricultural ecosystem and synthesizes their commercial uses in agriculture. Microbiota in agro-ecosystem works by nutrient acquisition, enhancing nutrient availability, water uptake, and amelioration of abiotic and abiotic stresses. External application of such beneficial microbiota or microbial consortia helps in boosting plant growth and provides resistance to drought, salinity, heavy metal, high-temperature and radiation stress in various crop plants. These have been instrumental in enhancing tolerance to diseases, insect pest and nematodes in various cropping system. However, studies on the microbiome in revolutionary production systems like conservation agriculture and protected cultivation, which use lesser agrochemicals, are limited and if exploited can provide valuable input in sustainable agriculture production.

Phytoremediation and Microorganisms-Assisted Phytoremediation of Mercury-Contaminated Soils: Challenges and Perspectives

Mercury (Hg) pollution is a global threat to human and environmental health because of its toxicity, mobility and long-term persistence. Although costly engineering-based technologies can be used to treat heavily Hg-contaminated areas, they are not suitable for decontaminating agricultural or extensively-polluted soils. Emerging phyto- and bioremediation strategies for decontaminating Hg-polluted soils generally involve low investment, simple operation, and in situ application, and they are less destructive for the ecosystem. Current understanding of the uptake, translocation and sequestration of Hg in plants is reviewed to highlight new avenues for exploration in phytoremediation research, and different phytoremediation strategies (phytostabilization, phytoextraction and phytovolatilization) are discussed. Research aimed at identifying suitable plant species and associated-microorganisms for use in phytoremediation of Hg-contaminated soils is also surveyed. Investigation into the potential use of transgenic plants in Hg-phytoremediation is described. Recent research on exploiting the beneficial interactions between plants and microorganisms (bacteria and fungi) that are Hg-resistant and secrete plant growth promoting compounds is reviewed. We highlight areas where more research is required into the effective use of phytoremediation on Hg-contaminated sites, and conclude that the approaches it offers provide considerable potential for the future.

A Cross-Metabolomic Approach Shows that Wheat Interferes with Fluorescent Pseudomonas Physiology through Its Root Metabolites

Roots contain a wide variety of secondary metabolites. Some of them are exudated in the rhizosphere, where they are able to attract and/or control a large diversity of microbial species. In return, the rhizomicrobiota can promote plant health and development. Some rhizobacteria belonging to the Pseudomonas genus are known to produce a wide diversity of secondary metabolites that can exert a biological activity on the host plant and on other soil microorganisms. Nevertheless, the impact of the host plant on the production of bioactive metabolites by Pseudomonas is still poorly understood. To characterize the impact of plants on the secondary metabolism of Pseudomonas, a cross-metabolomic approach has been developed. Five different fluorescent Pseudomonas strains were thus cultivated in the presence of a low concentration of wheat root extracts recovered from three wheat genotypes. Analysis of our metabolomic workflow revealed that the production of several Pseudomonas secondary metabolites was significantly modulated when bacteria were cultivated with root extracts, including metabolites involved in plant-beneficial properties.

Transcriptome profiling reveals the effects of drought tolerance in Giant Juncao

BACKGROUND

Giant Juncao is often used as feed for livestock because of its huge biomass. However, drought stress reduces forage production by affecting the normal growth and development of plants. Therefore, investigating the molecular mechanisms of drought tolerance will provide important information for the improvement of drought tolerance in this grass.

RESULTS

A total of 144.96 Gb of clean data was generated and assembled into 144,806 transcripts and 93,907 unigenes. After 7 and 14 days of drought stress, a total of 16,726 and 46,492 differentially expressed genes (DEGs) were observed, respectively. Compared with normal irrigation, 16,247, 23,503, and 11,598 DEGs were observed in 1, 5, and 9 days following rehydration, respectively. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed abiotic stress-responsive genes and pathways related to catalytic activity, methyltransferase activity, transferase activity, and superoxide metabolic process. We also identified transcription factors belonging to several families, including basic helix-loop-helix (bHLH), WRKY, NAM (no apical meristem), ATAF1/2 and CUC2 (cup-shaped cotyledon) (NAC), fatty acyl-CoA reductase (FAR1), B3, myeloblastosis (MYB)-related, and basic leucine zipper (bZIP) families, which are important drought-rehydration-responsive proteins. Weighted gene co-expression network analysis was also used to analyze the RNA-seq data to predict the interrelationship between genes. Twenty modules were obtained, and four of these modules may be involved in photosynthesis and plant hormone signal transduction that respond to drought and rehydration conditions.

CONCLUSIONS

Our research is the first to provide a more comprehensive understanding of DEGs involved in drought stress at the transcriptome level in Giant Juncao with different drought and recovery conditions. These results may reveal insights into the molecular mechanisms of drought tolerance in Giant Juncao and provide diverse genetic resources involved in drought tolerance research.

Insights into the early stages of plant-endophytic bacteria interaction

The plant holobiont is a complex entity composed of the plant and the organisms that live in and on it including its microbiota. The plant microbiota includes, among other microorganisms, bacterial endophytes, which are bacteria that can invade living plant tissues without causing symptoms of disease. The interaction between the endophytic bacterial microbiota and their plant host has profound influences on their fitness and depends on biotic and abiotic factors. For these interactions to be established, the bacteria have to be present at the right time, in the right place either colonizing the soil or the seed. In this review we summarize the current knowledge regarding the sources of the bacterial endophytic microbiome and the processes involved in the assemblage of the resulting community during the initial stages of plant development. The adaptations that allow the spatial approximation of soil- and seed-borne bacteria towards infection and colonization of the internal tissues of plants will be addressed in this review.

Specific PP2A Catalytic Subunits Are a Prerequisite for Positive Growth Effects in Arabidopsis Co-Cultivated with Azospirillum brasilense and Pseudomonas simiae

Plant growth-promoting rhizobacteria (PGPR) stimulate plant growth, but the underlying mechanism is poorly understood. In this study, we asked whether PROTEIN PHOSPHATASE 2A (PP2A), a regulatory molecular component of stress, growth, and developmental signaling networks in plants, contributes to the plant growth responses induced by the PGPR Azospirillum brasilense (wild type strain Sp245 and auxin deficient strain FAJ0009) and Pseudomonas simiae (WCS417r). The PGPR were co-cultivated with Arabidopsis wild type (WT) and PP2A (related) mutants. These plants had mutations in the PP2A catalytic subunits (C), and the PP2A activity-modulating genes LEUCINE CARBOXYL METHYL TRANSFERASE 1 (LCMT1) and PHOSPHOTYROSYL PHOSPHATASE ACTIVATOR (PTPA). When exposed to the three PGPR, WT and all mutant Arabidopsis revealed the typical phenotype of PGPR-treated plants with shortened primary root and increased lateral root density. Fresh weight of plants generally increased when the seedlings were exposed to the bacteria strains, with the exception of catalytic subunit double mutant c2c5. The positive effect on root and shoot fresh weight was especially pronounced in Arabidopsis mutants with low PP2A activity. Comparison of different mutants indicated a significant role of the PP2A catalytic subunits C2 and C5 for a positive response to PGPR.

What Did We Learn From Plant Growth-Promoting Rhizobacteria (PGPR)-Grass Associations Studies Through Proteomic and Metabolomic Approaches?

Plant growth stimulation by microorganisms that interact in a mutually beneficial manner remains poorly understood. Understanding the nature of plant-bacteria interactions may open new routes for plant productivity enhancement, especially cereal crops consumed by humans. Proteomic and metabolomic analyses are particularly useful for elucidating these mechanisms. A complete depiction of these mechanisms will prompt researchers to develop more efficient plant-bacteria associations. The success of microorganisms as biofertilizers may replace the current massive use of chemical fertilizers, mitigating many environmental and economic issues. In this review, we discuss the recent advances and current state of the art in proteomics and metabolomics studies involving grass-bacteria associations. We also discuss essential subjects involved in the bacterial plant-growth promotion, such, nitrogen fixation, plant stress, defense responses, and siderophore production.

The invisible life inside plants: Deciphering the riddles of endophytic bacterial diversity

Endophytic bacteria often promote plant growth and protect their host plant against pathogens, herbivores, and abiotic stresses including drought, increased salinity or pollution. Current agricultural practices are being challenged in terms of climate change and the ever-increasing demand for food. Therefore, the rational exploitation of bacterial endophytes to increase the productivity and resistance of crops appears to be very promising. However, the efficient and larger-scale use of bacterial endophytes for more effective and sustainable agriculture is hindered by very little knowledge on molecular aspects of plant-endophyte interactions and mechanisms driving bacterial communities in planta. In addition, since most of the information on bacterial endophytes has been obtained through culture-dependent techniques, endophytic bacterial diversity and its full biotechnological potential still remain highly unexplored. In this study, we discuss the diversity and role of endophytic populations as well as complex interactions that the endophytes have with the plant and vice versa, including the interactions leading to plant colonization. A description of biotic and abiotic factors influencing endophytic bacterial communities is provided, along with a summary of different methodologies suitable for determining the diversity of bacterial endophytes, mechanisms governing the assembly and structure of bacterial communities in the endosphere, and potential biotechnological applications of endophytes in the future.

Bacterial community characterization of the rhizobiome of plants belonging to Solanaceae family cultivated in desert soils

Purpose

The plant Solanaceae family is one of the most important for global agriculture and nutrition. Within this plant family, two plant species stand out for their economic importance and for human consumption, which are tomato (Solanum lycopersicum) and chili pepper (Capsicum annuum). Moreover, those plants support diverse and characteristic microbial communities that are uniquely suited to the plant habitat and intimately connected to plant health. The main objective of this work is the bacterial community characterization in the rhizobiome of tomato and chili pepper, cultivated in arid environments.

Methods

Five crop fields located in the south of the peninsula of Baja California, Mexico, were sampled. Total DNA was extracted from rhizosphere, rhizoplane, and endophytic root compartment and sequenced by Illumina MiniSeq platform technology applied to 16S rRNA gene V3 region.

Results

We were able to obtain 1,195,426 total reads and 1,725,258 total reads for tomato and chili pepper samples, respectively. The analysis of the bacterial community structures confirmed that the two plant species showed differences in their microbial community structures. Nonetheless, the microbial community structures were directly and equally influenced by the crop field localization of each plant species. Interestingly, we determined that in both plant species, the Proteobacteria was the main phylum.

Conclusion

In conclusion, we found that several bacterial families are part of the core rhizobiome (28 OTUs) for both tomato and chili pepper, but the most abundant were the Pseudomonadaceae family and the Pseudomonas genus, which most probably play a pivotal role in the microbial ecology to benefit both crop plants.

The combined analysis as the best strategy for Dual RNA-Seq mapping

In Dual RNA-Seq experiments the simultaneous extraction of RNA and analysis of gene expression data from both interacting organisms could be a challenge. One alternative is separating the reads during in silico data analysis. There are two main mapping methods used: sequential and combined. Here we present a combined approach in which the libraries were aligned to a concatenated genome to sort the reads before mapping them to the respective annotated genomes. A comparison of this method with the sequential analysis was performed. Two RNA-Seq libraries available in public databases consisting of a eukaryotic (Zea mays) and a prokaryotic (Herbaspirillum seropediceae) organisms were mixed to simulate a Dual RNA-Seq experiment. Libraries from real Dual RNA-Seq experiments were also used. The sequential analysis consistently attributed more reads to the first reference genome used in the analysis (due to cross-mapping) than the combined approach. More importantly, the combined analysis resulted in lower numbers of cross-mapped reads. Our results highlight the necessity of combining the reference genomes to sort reads previously to the counting step to avoid losing information in Dual RNA-Seq experiments. Since most studies first map the RNA-Seq libraries to the eukaryotic genome, much prokaryotic information has probably been lost.

Assessment of the structural and functional diversities of plant microbiota: Achievements and challenges - A review

Analyses of the spatial localization and the functions of bacteria in host plant habitats through in situ identification by immunological and molecular genetic techniques combined with high resolving microscopic tools and 3D-image analysis contributed substantially to a better understanding of the functional interplay of the microbiota in plants. Among the molecular genetic methods, 16S-rRNA genes were of central importance to reconstruct the phylogeny of newly isolated bacteria and to localize them in situ. However, they usually do not allow resolution for phylogenetic affiliations below genus level. Especially, the separation of opportunistic human pathogens from plant beneficial strains, currently allocated to the same species, needs genome-based resolving techniques. Whole bacterial genome sequences allow to discriminate phylogenetically closely related strains. In addition, complete genome sequences enable strain-specific monitoring for biotechnologically relevant strains. In this mini-review we present high resolving approaches for analysis of the composition and key functions of plant microbiota, focusing on interactions of diazotrophic plant growth promoting bacteria, like Azospirillum brasilense, with non-legume host plants. Combining high resolving microscopic analyses with specific immunological detection methods and molecular genetic tools, including especially transcriptome analyses of both the bacterial and plant partners, enables new insights into key traits of beneficial bacteria-plant interactions in holobiontic systems.

Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments

Bacterial pathogens subvert host cells by manipulating cellular pathways for survival and replication; in turn, host cells respond to the invading pathogen through cascading changes in gene expression. Deciphering these complex temporal and spatial dynamics to identify novel bacterial virulence factors or host response pathways is crucial for improved diagnostics and therapeutics. Dual RNA sequencing (dRNA-Seq) has recently been developed to simultaneously capture host and bacterial transcriptomes from an infected cell. This approach builds on the high sensitivity and resolution of RNA sequencing technology and is applicable to any bacteria that interact with eukaryotic cells, encompassing parasitic, commensal or mutualistic lifestyles. Several laboratory protocols have been presented that outline the collection, extraction and sequencing of total RNA for dRNA-Seq experiments, but there is relatively little guidance available for the detailed bioinformatic analyses required. This protocol outlines a typical dRNA-Seq experiment, based on a Chlamydia trachomatis-infected host cell, with a detailed description of the necessary bioinformatic analyses with currently available software tools.

Biocontrol of Cereal Crop Diseases Using Streptomycetes

A growing world population and an increasing demand for greater food production requires that crop losses caused by pests and diseases are dramatically reduced. Concurrently, sustainability targets mean that alternatives to chemical pesticides are becoming increasingly desirable. Bacteria in the plant root microbiome can protect their plant host against pests and pathogenic infection. In particular, Streptomyces species are well-known to produce a range of secondary metabolites that can inhibit the growth of phytopathogens. Streptomyces are abundant in soils and are also enriched in the root microbiomes of many different plant species, including those grown as economically and nutritionally valuable cereal crops. In this review we discuss the potential of Streptomyces to protect against some of the most damaging cereal crop diseases, particularly those caused by fungal pathogens. We also explore factors that may improve the efficacy of these strains as biocontrol agents in situ, as well as the possibility of exploiting plant mechanisms, such as root exudation, that enable the recruitment of microbial species from the soil to the root microbiome. We argue that a greater understanding of these mechanisms may enable the development of protective plant root microbiomes with a greater abundance of beneficial bacteria, such as Streptomyces species.

Defining the Genetic Basis of Plant⁻Endophytic Bacteria Interactions

Endophytic bacteria, which interact closely with their host, are an essential part of the plant microbiome. These interactions enhance plant tolerance to environmental changes as well as promote plant growth, thus they have become attractive targets for increasing crop production. Numerous studies have aimed to characterise how endophytic bacteria infect and colonise their hosts as well as conferring important traits to the plant. In this review, we summarise the current knowledge regarding endophytic colonisation and focus on the insights that have been obtained from the mutants of bacteria and plants as well as ‘omic analyses. These show how endophytic bacteria produce various molecules and have a range of activities related to chemotaxis, motility, adhesion, bacterial cell wall properties, secretion, regulating transcription and utilising a substrate in order to establish a successful interaction. Colonisation is mediated by plant receptors and is regulated by the signalling that is connected with phytohormones such as auxin and jasmonic (JA) and salicylic acids (SA). We also highlight changes in the expression of small RNAs and modifications of the cell wall properties. Moreover, in order to exploit the beneficial plant-endophytic bacteria interactions in agriculture successfully, we show that the key aspects that govern successful interactions remain to be defined.

Dual RNA-seq of Xanthomonas oryzae pv. oryzicola infecting rice reveals novel insights into bacterial-plant interaction

The Gram-negative bacterium Xanthomonas oryzae pv. oryzicola (Xoc) is the causal agent of rice bacterial leaf streak (BLS), one of the most destructive diseases of rice (Oryza sativa L.) that is the important staple crop. Xoc can invade host leaves via stomata and wounds and its type three secretion system (T3SS) is pivotal to its pathogenic lifestyle. In this study, using a novel dual RNA-seq approach, we examined transcriptomes of rice and Xoc in samples inoculated with wild type Xoc GX01 and its T3SS defective strain (T3SD), to investigate the global transcriptional changes in both organisms. Compared with T3SD strain, rice inoculated with wild type Xoc GX01 resulted in significant expression changes of a series of plant defence related genes, including ones altered in plant signalling pathway, and downregulated in phenylalanine metabolism, flavonoid and momilactone biosynthesis, suggesting repression of plant defence response and reduction in both callose deposition and phytoalexin accumulation. Also, some known transcription activator-like effector (TALE) targets were induced by Xoc GX01, e.g. OsSultr3;6 which contributes to rice susceptibility. Some cell elongation related genes, including several expansin genes, were induced by GX01 too, suggesting that Xoc may exploit this pathway to weaken cell wall strength, beneficial for bacterial infection. On the other hand, compared with wild type, the T3SD strain transcriptome in planta was characterized by downregulation of ATP, protein and polysaccharide synthesis, and upregulation of antioxidation and detoxification related genes, revealing that T3SD strain faced serious starvation and oxidation stresses in planta without a functional T3SS. In addition, comparative global transcript profiles of Xoc in planta and in medium revealed an upregulation of virulence factor synthesis and secretion in planta in favour of bacterial infection. Collectively, this study provides a comprehensive representation of cross talk between the host and bacterial pathogen, revealing insights into the Xoc-rice pathogenic dynamic and reveals novel strategies exploited by this important pathogen to cause disease.

The ammonium transporter AmtB and the PII signal transduction protein GlnZ are required to inhibit DraG in Azospirillum brasilense

The ammonium-dependent posttranslational regulation of nitrogenase activity in Azospirillum brasilense requires dinitrogenase reductase ADP-ribosyl transferase (DraT) and dinitrogenase reductase ADP-glycohydrolase (DraG). These enzymes are reciprocally regulated by interaction with the PII proteins, GlnB and GlnZ. In this study, purified ADP-ribosylated Fe-protein was used as substrate to study the mechanism involved in the regulation of A. brasilense DraG in vitro. The data show that DraG is partially inhibited by GlnZ and that DraG inhibition is further enhanced by the simultaneous presence of GlnZ and AmtB. These results are the first to demonstrate experimentally that DraG inactivation requires the formation of a ternary DraG-GlnZ-AmtB complex in vitro. Previous structural data have revealed that when the DraG-GlnZ complex associates with AmtB, the flexible T-loops of the trimeric GlnZ bind to AmtB and become rigid; these molecular events stabilize the DraG-GlnZ complex, resulting in DraG inactivation. To determine whether restraining the flexibility of the GlnZ T-loops is a limiting factor in DraG inhibition, we used a GlnZ variant that carries a partial deletion of the T-loop (GlnZΔ42-54). However, although the GlnZΔ42-54 variant was more effective in inhibiting DraG in vitro, it bound to DraG with a slightly lower affinity than does wild-type GlnZ and was not competent to completely inhibit DraG activity either in vitro or in vivo. We, therefore, conclude that the formation of a ternary complex between DraG-GlnZ-AmtB is necessary for the inactivation of DraG.

De novo assembly of wheat root transcriptomes and transcriptional signature of longitudinal differentiation

Hidden underground, root systems constitute an important part of the plant for its development, nourishment and sensing the soil environment around it, but we know very little about its genetic regulation in crop plants like wheat. In the present study, we de novo assembled the root transcriptomes in reference cultivar Chinese Spring from RNA-seq reads generated by the 454-GS-FLX and HiSeq platforms. The FLX reads were assembled into 24,986 transcripts with completeness of 54.84%, and the HiSeq reads were assembled into 91,543 high-confidence protein-coding transcripts, 2,404 low-confidence protein-coding transcripts, and 13,181 non-coding transcripts with the completeness of >90%. Combining the FLX and HiSeq assemblies, we assembled a root transcriptome of 92,335 ORF-containing transcripts. Approximately 7% of the coding transcripts and ~2% non-coding transcripts are not present in the current wheat genome assembly. Functional annotation of both assemblies showed similar gene ontology patterns and that ~7% coding and >5% non-coding transcripts are root-specific. Transcription quantification identified 1,728 differentially expressed transcripts between root tips and maturation zone, and functional annotation of these transcripts captured a transcriptional signature of longitudinal development of wheat root. With the transcriptomic resources developed, this study provided the first view of wheat root transcriptome under different developmental zones and laid a foundation for molecular studies of wheat root development and growth using a reverse genetic approach.