Plant-Influenced Gene Expression in the Rice Endophyte Burkholderia kururiensis M130

Biocontrol of plant pathogens in omics era-with special focus on endophytic bacilli

Nearly all plants and their organs are inhabited by endophytic microbes which play a crucial role in plant fitness and stress resilience. Harnessing endophytic services can provide effective solutions for a sustainable increase in agriculture productivity and can be used as a complement or alternative to agrochemicals. Shifting agriculture practices toward the use of nature-based solutions can contribute directly to the global challenges of food security and environmental sustainability. However, microbial inoculants have been used in agriculture for several decades with inconsistent efficacy. Key reasons of this inconsistent efficacy are linked to competition with indigenous soil microflora and inability to colonize plants. Endophytic microbes provide solutions to both of these issues which potentially make them better candidates for microbial inoculants. This article outlines the current advancements in endophytic research with special focus on endophytic bacilli. A better understanding of diverse mechanisms of disease control by bacilli is essential to achieve maximum biocontrol efficacy against multiple phytopathogens. Furthermore, we argue that integration of emerging technologies with strong theoretical frameworks have the potential to revolutionize biocontrol approaches based on endophytic microbes.

Bacteria from the skin of amphibians promote growth of Arabidopsis thaliana and Solanum lycopersicum by modifying hormone-related transcriptome response

Plants and microorganisms establish beneficial associations that can improve their development and growth. Recently, it has been demonstrated that bacteria isolated from the skin of amphibians can contribute to plant growth and defense. However, the molecular mechanisms involved in the beneficial effect for the host are still unclear. In this work, we explored whether bacteria isolated from three tropical frogs species can contribute to plant growth. After a wide screening, we identified three bacterial strains with high biostimulant potential, capable of modifying the root structure of Arabidopsis thaliana plants. In addition, applying individual bacterial cultures to Solanum lycopersicum plants induced an increase in their growth. To understand the effect that these microorganisms have over the host plant, we analysed the transcriptomic profile of A. thaliana during the interaction with the C32I bacterium, demonstrating that the presence of the bacteria elicits a transcriptional response associated to plant hormone biosynthesis. Our results show that amphibian skin bacteria can function as biostimulants to improve agricultural crops growth and development by modifying the plant transcriptomic responses.

Genetic Loci of Plant Pathogenic Dickeya solani IPO 2222 Expressed in Contact with Weed-Host Bittersweet Nightshade (Solanum dulcamara L.) Plants

Dickeya solani, belonging to the Soft Rot Pectobacteriaceae, are aggressive necrotrophs, exhibiting both a wide geographic distribution and a wide host range that includes many angiosperm orders, both dicot and monocot plants, cultivated under all climatic conditions. Little is known about the infection strategies D. solani employs to infect hosts other than potato (Solanum tuberosum L.). Our earlier study identified D. solani Tn5 mutants induced exclusively by the presence of the weed host S. dulcamara. The current study assessed the identity and virulence contribution of the selected genes mutated by the Tn5 insertions and induced by the presence of S. dulcamara. These genes encode proteins with functions linked to polyketide antibiotics and polysaccharide synthesis, membrane transport, stress response, and sugar and amino acid metabolism. Eight of these genes, encoding UvrY (GacA), tRNA guanosine transglycosylase Tgt, LPS-related WbeA, capsular biosynthesis protein VpsM, DltB alanine export protein, glycosyltransferase, putative transcription regulator YheO/PAS domain-containing protein, and a hypothetical protein, were required for virulence on S. dulcamara plants. The implications of D. solani interaction with a weed host, S. dulcamara, are discussed.

Bio Prospecting of Endophytes and PGPRs in Artemisinin Production for the Socio-economic Advancement

The growing demand for Artemisia annua plants in healthcare, food, and pharmaceutical industries has led to increased cultivation efforts to extract a vital compound, Artemisinin. The efficacy of Artemisinin as a potent drug against malaria disease is well established but its limited natural abundance. However, the common practice of using chemical fertilizers for maximum yield has adverse effects on plant growth, development, and the quality of phytochemicals. To address these issues, the review discusses the alternative approach of harnessing beneficial rhizosphere microbiota, particularly plant growth-promoting rhizobacteria (PGPR). Microbes hold substantial biotechnological potential for augmenting medicinal plant production, offering an environmentally friendly and cost-effective means to enhance medicinal plant production. This review article aims to identify a suitable endophytic population capable of enabling Artemisia sp. to thrive amidst abiotic stress while simultaneously enhancing Artemisinin production, thereby broadening its availability to a larger population. Furthermore, by subjecting endophytes to diverse combinations of harsh conditions, this review sheds light on the modulation of essential artemisinin biosynthesis pathway genes, both up regulated and down regulated. The collective findings suggest that through the in vitro engineering of endophytic communities and their in vivo application to Artemisia plants cultivated in tribal population fields, artemisinin production can be significantly augmented. The overall aim of this review to explore the potential of harnessing microbial communities, their functions, and services to enhance the cultivation of medicinal plants. It outlines a promising path toward bolstering artemisinin production, which holds immense promise in the fight against malaria.

Endophytic Seed-Associated Bacteria as Plant Growth Promoters of Cuban Rice (Oryza sativa L.)

Cuban rice cultivars INCA LP-5 and INCA LP-7 are widely distributed in Cuba and Caribbean countries. Although there are studies about rhizospheric bacteria associated with these cultivars, there are no reports about their seed-associated bacteria. This study aimed to isolate endophytic bacteria from rice seeds and select those with the greatest plant growth-promoting traits. A total of nineteen bacterial strains from the genera Pantoea, Bacillus, Paenibacillus, and Pseudomonas were isolated from the husk and endosperm of rice seeds. The strains Pantoea sp. S5-1, Pseudomonas sp. S5-38, and Pseudomonas sp. S7-1 were classified as the most promissory to increase rice growth as they demonstrated the presence of multiple plant growth-promoting traits such as the production of auxins, phosphate, and potassium solubilization, the production of siderophores, and the inhibition of the phytopathogen Pyricularia oryzae. The inoculation of strains of Pantoea sp. and Pseudomonas spp. in rice improves the height, root length, fresh weight, and dry weight of the shoot and root after 21 days post-inoculation in hydroponic assays. This study constitutes the first report on Cuban rice cultivars about the presence of endophytes in seeds and their potential to promote seedling growth. Pantoea sp. S5-1, Pseudomonas sp. S5-38, and Pseudomonas sp. S7-1 were selected as the more promising strains for the development of bio-stimulators or bio-inoculants for Cuban rice crops.

Enhancing Stevia rebaudiana growth and yield through exploring beneficial plant-microbe interactions and their impact on the underlying mechanisms and crop sustainability

Stevia rebaudiana is an important medicinal plant which represents the most important sugar substitute in many countries. Poor seed germination of this plant is a critical problem that affects the final yield and the availability of the products in the market. Continuous cropping without supplying soil nutrients is also a serious issue as it results in declining soil fertility. This review highlights the important use of beneficial bacteria for the enhancement of Stevia rebaudiana growth and its dynamic interactions in the phyllosphere, rhizosphere, and endosphere. Fertilizers can increase crop yield and preserve and improve soil fertility. There is a rising concern that prolonged usage of chemical fertilizers may have negative impacts on the ecosystem of the soil. On the other hand, soil health and fertility are improved by plant growth-promoting bacteria which could eventually increase plant growth and productivity. Accordingly, a biocompatible strategy involving beneficial microorganisms inoculation is applied to boost plant growth and reduce the negative effects of chemical fertilizers. Plants benefit extensively from endophytic bacteria, which promote growth and induce resistance to pathogens and stresses. Additionally, several plant growth-promoting bacteria are able to produce amino acids, polyamines, and hormones that can be used as alternatives to chemicals. Therefore, understanding the dynamic interactions between bacteria and Stevia can help make the favorable bacterial bio-formulations, use them more effectively, and apply them to Stevia to improve yield and quality.

Comparison of the colonization ability of Burkholderia strain B23 in the citrus rhizoplane and rhizosphere and assessment of the underlying mechanisms using full-length 16S rDNA amplicon and metatranscriptomic analyses

The characterization of bacterial strains with efficient root colonization ability and the mechanisms responsible for their efficient colonization is critical for the identification and application of beneficial bacteria. In this study, we found that Burkholderia strain B23 exhibited a strong niche differentiation between the rhizosphere and rhizoplane (a niche with more abundant easy-to-use nutrients but stronger selective pressures compared with the tightly adjacent rhizosphere) when inoculated into the field-grown citrus trees. Full-length 16S rDNA amplicon analysis demonstrated that the relative abundance of B23 in the rhizoplane microbiome at 3, 5, and 9 days post-inoculation (dpi) was always higher than that at 1 dpi, whereas its relative abundance in the rhizosphere microbiome was decreased continuously, as demonstrated by a 3.18-fold decrease at 9 dpi compared to 1 dpi. Time-series comparative expression profiling of B23 between the rhizoplane and rhizosphere was performed at representative time points (1, 3, and 9 dpi) through metatranscriptomic analysis, and the results demonstrated that multiple genes involved in the uptake and utilization of easy-to-use carbohydrates and amino acids and those involved in metabolism, energy production, replication, and translation were upregulated in the rhizoplane compared with the rhizosphere at 1 dpi and 3 dpi. Several genes involved in resistance to plant- and microbial competitor-derived stresses exhibited higher expression activities in the rhizoplane compared with the rhizosphere. Furthermore, gene loci responsible for the biosynthesis of the key antifungal and antibacterial metabolites occidiofungin and ornibactin were induced, and their expression levels remained relatively stable from 3 dpi to 9 dpi in the rhizoplane but not in the rhizosphere. Collectively, our findings provide novel lights into the mechanisms underlying the root colonization of the inoculated bacterial strains and serve as a basis for the identification of strains with efficient colonization ability, thus contributing to the development of beneficial bacteria applications.

Molecular identification and characterization of phytobeneficial osmotolerant endophytic bacteria inhabiting root nodules of the Saharan tree Vachellia tortilis subsp. raddiana

Nodular endophytes of drought-tolerant legumes are understudied. For this reason, we have isolated and studied non-symbiotic endophytic bacteria from nodules of Vachellia tortilis subsp. raddiana, a leguminous tree adapted to the harsh arid climate of Southern Morocco. Rep-PCR analysis followed by 16S rDNA sequencing revealed two main genera, Pseudomonas and Bacillus. Isolates responded variably to salt and water stresses, and mostly produced exopolysaccharides. Differences concerned also plant growth-promoting activities: phosphate, potassium, and zinc solubilization; biological nitrogen fixation; auxin, siderophore, ammonia, and HCN production; and ACC deaminase activity. Some strains exhibited antagonistic activities against phytopathogenic fungi (Fusarium oxysporum and Botrytis cinerea) and showed at least two enzymatic activities (cellulase, protease, chitinase). Four selected strains inoculated to vachellia plants under controlled conditions have shown significant positive impacts on plant growth parameters. These strains are promising bio-inoculants for vachellia plants to be used in reforestation programs in arid areas increasingly threatened by desertification.

Is Endophytic Colonization of Host Plants a Method of Alleviating Drought Stress? Conceptualizing the Hidden World of Endophytes

In the wake of changing climatic conditions, plants are frequently exposed to a wide range of biotic and abiotic stresses at various stages of their development, all of which negatively affect their growth, development, and productivity. Drought is one of the most devastating abiotic stresses for most cultivated crops, particularly in arid and semiarid environments. Conventional breeding and biotechnological approaches are used to generate drought-tolerant crop plants. However, these techniques are costly and time-consuming. Plant-colonizing microbes, notably, endophytic fungi, have received increasing attention in recent years since they can boost plant growth and yield and can strengthen plant responses to abiotic stress. In this review, we describe these microorganisms and their relationship with host plants, summarize the current knowledge on how they “reprogram” the plants to promote their growth, productivity, and drought tolerance, and explain why they are promising agents in modern agriculture.

Current Techniques to Study Beneficial Plant-Microbe Interactions

Many different experimental approaches have been applied to elaborate and study the beneficial interactions between soil bacteria and plants. Some of these methods focus on changes to the plant and others are directed towards assessing the physiology and biochemistry of the beneficial plant growth-promoting bacteria (PGPB). Here, we provide an overview of some of the current techniques that have been employed to study the interaction of plants with PGPB. These techniques include the study of plant microbiomes; the use of DNA genome sequencing to understand the genes encoded by PGPB; the use of transcriptomics, proteomics, and metabolomics to study PGPB and plant gene expression; genome editing of PGPB; encapsulation of PGPB inoculants prior to their use to treat plants; imaging of plants and PGPB; PGPB nitrogenase assays; and the use of specialized growth chambers for growing and monitoring bacterially treated plants.

Differential Genetic Strategies of Burkholderia vietnamiensis and Paraburkholderia kururiensis for Root Colonization of Oryza sativa subsp. japonica and O. sativa subsp. indica , as Revealed by Transposon Mutagenesis Sequencing

Burkholderiaceae are frequent and abundant colonizers of the rice rhizosphere and interesting candidates to investigate for growth promotion. Species of Paraburkholderia have repeatedly been described to stimulate plant growth.

What do we know from the transcriptomic studies investigating the interactions between plants and plant growth-promoting bacteria?

Major crops such as corn, wheat, and rice can benefit from interactions with various plant growth-promoting bacteria (PGPB). Naturally, several studies have investigated the primary mechanisms by which these PGPB promote plant growth. These mechanisms involve biological nitrogen fixation, phytohormone synthesis, protection against biotic and abiotic stresses, etc. Decades of genetic and biochemical studies in the legume-rhizobia symbiosis and arbuscular mycorrhizal symbiosis have identified a few key plant and microbial signals regulating these symbioses. Furthermore, genetic studies in legumes have identified the host genetic pathways controlling these symbioses. But, the same depth of information does not exist for the interactions between host plants and PGPB. For instance, our knowledge of the host genes and the pathways involved in these interactions is very poor. However, some transcriptomic studies have investigated the regulation of gene expression in host plants during these interactions in recent years. In this review, we discuss some of the major findings from these studies and discuss what lies ahead. Identifying the genetic pathway(s) regulating these plant-PGPB interactions will be important as we explore ways to improve crop production sustainably.

Morphological and physiological response of sour orange (Citrus aurantium L.) seedlings to the inoculation of taxonomically characterized bacterial endophytes

Entophytic bacteria (EBs) are very diverse and found in virtually all plant species studied. These natural EBs live insides the host plant and can be used to maximize crop and fruit yield by exploiting their potential. In this paper, EBs characterization from various citrus genotypes and their influence on the morphological and physiological functioning of sour orange (Citrus aurantium) seedlings are described. To assess the influence of 10 distinct EBs, three different techniques (injection, soil mix, and spray) were applied for single and mixed inoculation on sour orange (C. aurantium) seedlings. The selected strains were identified as firmicutes (Enterococcus faecalis, Bacillus safensis, Bacillus cereus, Bacillus megaterium, Brevibacillus borstelensis & Staphylococcus haemolyticus), and gamma Proteobacteria (Enterobacter hormachaei, Proteus mirabilis, Pseudomonas aeruginosa, & Pseudomonas sp.) by 16S rRNA gene sequencing. To investigate the influence of these EBs on host plant morphology, different parameters (morphometric) were recorded after five WOI (weeks of inoculation), including shoot/root length, shoot/root fresh and dry biomass, and biophysical analyses i.e., relative water content (RLWC). Physiological markers such as chlorophyll & carotenoid content, protein content, proline content, phenolics, and flavonoids were also analyzed to determine the influence of endophytes on sour orange seedlings. Five strains such as SM-34, SM-20, SM-36, SM-68, and SM-56 significantly improved the development and physiology of sour orange seedlings. Bacillus cereus and Pseudomonas aeruginosa produced the best outcomes in terms of plant growth. The relative quantification of bacterial inoculums was determined using real-time PCR. A rise in the number of bacterial cells in inoculated treatment suggests that bacterial strains survived and colonized successfully, and also shown their competitiveness with native bacterial community structure. As per the results of inoculation methods, soil mixing, and injection methods were determined to be effective for bacterial inoculation to plants but a variable trend was found for different parameters with test bacterial strains. After testing their impact on field conditions, these strains can be applied as fertilizers as an alternative to conventional chemical fertilizer, although in the context of mixed inoculation of bacterial strains, 5 M and 6 M performed best and enhanced plant growth-promoting activity.

The Threat of Pests and Pathogens and the Potential for Biological Control in Forest Ecosystems

Forests are an essential component of the natural environment, as they support biodiversity, sequester carbon, and play a crucial role in biogeochemical cycles—in addition to producing organic matter that is necessary for the function of terrestrial organisms. Forests today are subject to threats ranging from natural occurrences, such as lightning-ignited fires, storms, and some forms of pollution, to those caused by human beings, such as land-use conversion (deforestation or intensive agriculture). In recent years, threats from pests and pathogens, particularly non-native species, have intensified in forests. The damage, decline, and mortality caused by insects, fungi, pathogens, and combinations of pests can lead to sizable ecological, economic, and social losses. To combat forest pests and pathogens, biocontrol may be an effective alternative to chemical pesticides and fertilizers. This review of forest pests and potential adversaries in the natural world highlights microbial inoculants, as well as research efforts to further develop biological control agents against forest pests and pathogens. Recent studies have shown promising results for the application of microbial inoculants as preventive measures. Other studies suggest that these species have potential as fertilizers.

The Potential Application of Endophytes in Management of Stress from Drought and Salinity in Crop Plants

Endophytic microorganisms present inside the host plant play an essential role in host fitness, nutrient supply and stress tolerance. Endophytes are often used in sustainable agriculture as biofertilizers, biopesticides and as inoculants to mitigate abiotic stresses including salinity, drought, cold and pH variation in the soil. In changing climatic conditions, abiotic stresses create global challenges to achieve optimum crop yields in agricultural production. Plants experience stress conditions that involve endogenous boosting of their immune system or the overexpression of their defensive redox regulatory systems with increased reactive oxygen species (ROS). However, rising stress factors overwhelm the natural redox protection systems of plants, which leads to massive internal oxidative damage and death. Endophytes are an integral internal partner of hosts and have been shown to mitigate abiotic stresses via modulating local or systemic mechanisms and producing antioxidants to counteract ROS in plants. Advancements in omics and other technologies have been made, but potential application of endophytes remains largely unrealized. In this review article, we will discuss the diversity, population and interaction of endophytes with crop plants as well as potential applications in abiotic stress management.

Plant Growth Promoting and Stress Mitigating Abilities of Soil Born Microorganisms

Abiotic stresses affect the plant growth in different ways and at different developmental stages that reduce the crop yields. The increasing world population continually demands more crop yields; therefore it is important to use low-cost technologies against abiotic stresses to increase crop productivity. Soil microorganisms survive in the soil associated with plants in extreme condition. It was demonstrated that these beneficial microorganisms promote plant growth and development under various stresses. The soil microbes interact with the plant through rhizospheric or endophytic association and promote the plant growth through different processes such as nutrients mobilization, disease suppression, and hormone secretions. The microorganisms colonized in the rhizospheric region and imparted the abiotic stress tolerance by producing 1-aminocyclopropane-1- carboxylate (ACC) deaminase, antioxidant, and volatile compounds, inducing the accumulation of osmolytes, production of exopolysaccharide, upregulation or downregulation of stress genes, phytohormones and change the root morphology. A large number of these rhizosphere microorganisms are now patented. In the present review, an attempt was made to throw light on the mechanism of micro-organism that operates during abiotic stresses and promotes plant survival and productivity.

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.

Bacterial endophytome-mediated resistance in banana for the management of Fusarium wilt

Banana (Musa spp.), a major cash and staple fruit crop in many parts of the world, is infected by Fusarium wilt, which contributes up to 100% yield loss and causes social consequences. Race 1 and race 2 of Panama wilt caused by Fusarium oxysporum f. sp. cubense (Foc) are prevalent worldwide and seriously affect many traditional varieties. The threat of Foc tropical race 4 (Foc TR4) is looming large in African counties. However, its incidence in India has been confined to Bihar (Katihar and Purnea), Uttar Pradesh (Faizabad), Madhya Pradesh (Burhanpur) and Gujarat (Surat). Management of Foc races by employing fungicides is often not a sustainable option as the disease spread is rapid and they negatively alter the biodiversity of beneficial ectophytes and endophytes. Besides, soil drenching with carbendazim/trifloxystrobin + tebuconazole is also not effective in suppressing the Fusarium wilt of banana. Improvement of resistance to Fusarium wilt in susceptible cultivars is being addressed through both conventional and advanced breeding approaches. However, engineering of banana endosphere with bacterial endophytes from resistant genotypes like Pisang lilly and YKM5 will induce the immune response against Foc, irrespective of races. The composition of the bacterial endomicrobiome in different banana cultivars is dominated by the phyla Proteobacteria, Bacteroidetes and Actinobacteria. The major bacterial endophytic genera antagonistic to Foc are Bacillus, Brevibacillus, Paenibacillus, Virgibacillus, Staphylococcus, Cellulomonas, Micrococcus, Corynebacterium, Kocuria spp., Paracoccus sp., Acinetobacter spp. Agrobacterium, Aneurinibacillus, Enterobacter, Klebsiella, Lysinibacillus, Micrococcus, Rhizobium, Sporolactobacillus, Pantoea, Pseudomonas, Serratia, Microbacterium, Rhodococcus, Stenotrophomonas, Pseudoxanthomonas, Luteimonas, Dokdonella, Rhodanobacter, Luteibacter, Steroidobacter, Nevskia, Aquicella, Rickettsiella, Legionella, Tatlockia and Streptomyces. These bacterial endophytes promote the growth of banana plantlets by solubilising phosphate, producing indole acetic acid and siderophores. Application of banana endophytes during the hardening phase of tissue-cultured clones serves as a shield against Foc. Hitherto, MAMP molecules of endophytes including flagellin, liposaccharides, peptidoglycans, elongation factor, cold shock proteins and hairpins induce microbe-associated molecular pattern (MAMP)-triggered immunity to suppress plant pathogens. The cascade of events associated with ISR and SAR is induced through MAPK and transcription factors including WRKY and MYC. Studies are underway to exploit the potential of antagonistic bacterial endophytes against Foc isolates and to develop an understanding of the MAMP-triggered immunity and metabolomics cross talk modulating resistance. This review explores the possibility of harnessing the potential bacterial endomicrobiome against Foc and developing nanoformulations with bacterial endophytes for increased efficacy against lethal pathogenic races of Foc infecting banana.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02833-5.

Bacterial Endophytes: The Hidden Actor in Plant Immune Responses against Biotic Stress

Bacterial endophytes constitute an essential part of the plant microbiome and are described to promote plant health by different mechanisms. The close interaction with the host leads to important changes in the physiology of the plant. Although beneficial bacteria use the same entrance strategies as bacterial pathogens to colonize and enter the inner plant tissues, the host develops strategies to select and allow the entrance to specific genera of bacteria. In addition, endophytes may modify their own genome to adapt or avoid the defense machinery of the host. The present review gives an overview about bacterial endophytes inhabiting the phytosphere, their diversity, and the interaction with the host. Direct and indirect defenses promoted by the plant-endophyte symbiont exert an important role in controlling plant defenses against different stresses, and here, more specifically, is discussed the role against biotic stress. Defenses that should be considered are the emission of volatiles or antibiotic compounds, but also the induction of basal defenses and boosting plant immunity by priming defenses. The primed defenses may encompass pathogenesis-related protein genes (PR family), antioxidant enzymes, or changes in the secondary metabolism.

Bacterial endophytes: Molecular interactions with their hosts

Plant growth promotion has been found associated with plants on the surface (epiphytic), inside (endophytic), or close to the plant roots (rhizospheric). Endophytic bacteria mainly have been researched for their beneficial activities in terms of nutrient availability, plant growth hormones, and control of soil-borne and systemic pathogens. Molecular communications leading to these interactions between plants and endophytic bacteria are now being unrevealed using multidisciplinary approaches with advanced techniques such as metagenomics, metaproteomics, metatranscriptomics, metaproteogenomic, microRNAs, microarray, chips as well as the comparison of complete genome sequences. More than 400 genes in both the genomes of host plant and bacterial endophyte are up- or downregulated for the establishment of endophytism and plant growth-promoting activity. The involvement of more than 20 genes for endophytism, about 50 genes for direct plant growth promotion, about 25 genes for biocontrol activity, and about 10 genes for mitigation of different stresses has been identified in various bacterial endophytes. This review summarizes the progress that has been made in recent years by these modern techniques and approaches.

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.

Transcriptomic and Metabolomic Approaches Deepen Our Knowledge of Plant-Endophyte Interactions

In natural systems, plant-symbiont-pathogen interactions play important roles in mitigating abiotic and biotic stresses in plants. Symbionts have their own special recognition ways, but they may share some similar characteristics with pathogens based on studies of model microbes and plants. Multi-omics technologies could be applied to study plant-microbe interactions, especially plant-endophyte interactions. Endophytes are naturally occurring microbes that inhabit plants, but do not cause apparent symptoms in them, and arise as an advantageous source of novel metabolites, agriculturally important promoters, and stress resisters in their host plants. Although biochemical, physiological, and molecular investigations have demonstrated that endophytes confer benefits to their hosts, especially in terms of promoting plant growth, increasing metabolic capabilities, and enhancing stress resistance, plant-endophyte interactions consist of complex mechanisms between the two symbionts. Further knowledge of these mechanisms may be gained by adopting a multi-omics approach. The involved interaction, which can range from colonization to protection against adverse conditions, has been investigated by transcriptomics and metabolomics. This review aims to provide effective means and ways of applying multi-omics studies to solve the current problems in the characterization of plant-microbe interactions, involving recognition and colonization. The obtained results should be useful for identifying the key determinants in such interactions and would also provide a timely theoretical and material basis for the study of interaction mechanisms and their applications.

High-throughput sequencing-based analysis of the composition and diversity of endophytic bacterial community in seeds of upland rice

Upland rice is an ecotype crop resulting from the long-term domestication and evolution of rice in dry land without a water layer. Generally, the stems and leaves are thick and luxuriant, while the leaves also typically broad and light. The root system is developed with abundant root hair, and the osmotic pressure of the root and cell juice concentration in the leaves is high, while this plant is drought-resistant, heat-resistant, and water absorbent. This study aims to reveal the "core flora" of the endophytes in upland rice seeds by examining their diversity and community structures. It further intends to reveal the impact of the soil environment on the formation of endophyte community structures in upland rice seeds by comparing the environmental soil microorganisms in upland rice habitats. In this study, high-throughput sequencing technology based on the Illumina Hiseq 2500 platform was used to investigate the structure and diversity of endophytic bacterial communities using upland rice varieties collected from different locations and soil samples from unified planting sites as materials. Here, 42 endophytic OTUs were found to coexist in the 14 samples. At the phylum level, the first dominant phyla in all the samples were Proteobacteria (93.81-99.99%). At the genus level, Pantoea (8.77-87.77%), Pseudomonas (1.15-61.58%), Methylobacterium (0.40-4.64%), Sphingomonas (0.26-3.85%), Microbacterium (0.01-4.67%) and Aurantimonas (0.04-4.34%), which represent the core microflora in upland rice seeds, served as the dominant genera that coexisted in all the upland rice seeds tested. This study significant for the isolation, screening, functional evaluation, and re-action of various functional microorganisms in upland rice to improve its agronomic traits. It also provides a specific reference for the interaction between microorganisms and plants.

Deciphering the Omics of Plant-Microbe Interaction: Perspectives and New Insights

Introduction

Plants do not grow in isolation, rather they are hosts to a variety of microbes in their natural environments. While, few thrive in the plants for their own benefit, others may have a direct impact on plants in a symbiotic manner. Unraveling plant-microbe interactions is a critical component in recognizing the positive and negative impacts of microbes on plants. Also, by affecting the environment around plants, microbes may indirectly influence plants. The progress in sequencing technologies in the genomics era and several omics tools has accelerated in biological science. Studying the complex nature of plant-microbe interactions can offer several strategies to increase the productivity of plants in an environmentally friendly manner by providing better insights. This review brings forward the recent works performed in building omics strategies that decipher the interactions between plant-microbiome. At the same time, it further explores other associated mutually beneficial aspects of plant-microbe interactions such as plant growth promotion, nitrogen fixation, stress suppressions in crops and bioremediation; as well as provides better insights on metabolic interactions between microbes and plants through omics approaches. It also aims to explore advances in the study of Arabidopsis as an important avenue to serve as a baseline tool to create models that help in scrutinizing various factors that contribute to the elaborate relationship between plants and microbes. Causal relationships between plants and microbes can be established through systematic gnotobiotic experimental studies to test hypotheses on biologically derived interactions.

Conclusion

This review will cover recent advances in the study of plant-microbe interactions keeping in view the advantages of these interactions in improving nutrient uptake and plant health.

Genome-Wide Identification of Dickeya solani Transcriptional Units Up-Regulated in Response to Plant Tissues From a Crop-Host Solanum tuberosum and a Weed-Host Solanum dulcamara

Dickeya solani is a Gram-negative bacterium able to cause disease symptoms on a variety of crop and ornamental plants worldwide. Weeds including Solanum dulcamara (bittersweet nightshade) growing near agricultural fields have been reported to support populations of soft rot bacteria in natural settings. However, little is known about the specific interaction of D. solani with such weed plants that may contribute to its success as an agricultural pathogen. The aim of this work was to assess the interaction of D. solani with its crop plant (Solanum tuberosum) and an alternative (S. dulcamara) host plant. From a collection of 10,000 Tn5 transposon mutants of D. solani IPO2222 carrying an inducible, promotorless gusA reporter gene, 210 were identified that exhibited plant tissue-dependent expression of the gene/operon into which the Tn5 insertion had occurred. Thirteen Tn5 mutants exhibiting the greatest plant tissue induction of such transcriptional units in S. tuberosum or S. dulcamara as measured by qRT-PCR were assessed for plant host colonization, virulence, and ability to macerate plant tissue, as well as phenotypes likely to contribute to the ecological fitness of D. solani, including growth rate, carbon and nitrogen source utilization, motility, chemotaxis toward plant extracts, biofilm formation, growth under anaerobic conditions and quorum sensing. These 13 transcriptional units encode proteins involved in bacterial interactions with plants, with functions linked to cell envelope structure, chemotaxis and carbon metabolism. The selected 13 genes/operons were differentially expressed in, and thus contributed preferentially to D. solani fitness in potato and/or S. dulcamara stem, leaf, and root tissues.

Screening of Bacterial Endophytes Able to Promote Plant Growth and Increase Salinity Tolerance

Bacterial endophytes can colonize plant tissues without harming the plant. Instead, they are often able to increase plant growth and tolerance to environmental stresses. In this work, new strains of bacterial endophytes were isolated from three economically important crop plants (sorghum, cucumber and tomato) grown in three different regions in soils with different management. All bacterial strains were identified by 16S rRNA sequencing and characterized for plant beneficial traits. Based on physiological activities, we selected eight strains that were further tested for their antibiotic resistance profile and for the ability to efficiently colonize the interior of sorghum plants. According to the results of the re-inoculation test, five strains were used to inoculate sorghum seeds. Then, plant growth promotion activity was assessed on sorghum plants exposed to salinity stress. Only two bacterial endophytes increased plant biomass, but three of them delayed or reduced plant salinity stress symptoms. These five strains were then characterized for the ability to produce the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which is involved in the increase of stress tolerance. Pseudomonas brassicacearum SVB6R1 was the only strain that was able to produce this enzyme, suggesting that ACC deaminase is not the only physiological trait involved in conferring plant tolerance to salt stress in these bacterial strains.

Endophytes: Colonization, Behaviour, and Their Role in Defense Mechanism

Biotic and abiotic factors cause an enormous amount of yield and economical loss. However, endophytes can play a significant role in enhancing the tolerance of plants. Endophytes systematically colonize different parts of the host, but plants use a variety of defense mechanisms towards microbial infection. However, they have to survive the oxidative environments, and endophytes like Enterobacter sp. encode superoxide dismutases, catalases, and hydroperoxide reductases to cope up the oxidative stress during colonization. On the contrary, others produce subtilomycin which binds with flagella to affect flg22-induced plant defense. The behavior of endophytes can be affected by different genes in hydrolase activity when they come into contact with the host plant. The lifestyle of endophytes is influenced by environmental factors, the host, and microbial genotypes, as well as an imbalance in nutrient exchange between the microbe and the host. For instance, induction of PiAMT1 in root endophyte Piriformospora indica indicates depletion of nitrogen which plays as a triggering factor for activation of the saprotrophic program. Microbes enhance disease resistance through induced systemic resistance (ISR), and Bacillus cereus triggers ISR against Botrytis cinerea through an accumulation of the PR1 protein and activates MAPK signaling and WRKY53 gene expression by the JA/ET signaling pathway. Similarly, Trichoderma arundinaceum produces trichodiene that affects Botrytis cinerea through induction of defense-related genes encoding salicylic acid (SA) and jasmonate (JA). Overall, endophytes can play a vital role in disease management.

Responses of Soybean Genes in the Substituted Segments of Segment Substitution Lines Following a Xanthomonas Infection

Bacterial blight, which is one of the most common soybean diseases, is responsible for considerable yield losses. In this study, a novel Xanthomonas vasicola strain was isolated from the leaves of soybean plants infected with bacterial blight under field conditions. Sequencing the X. vasicola genome revealed type-III effector-coding genes. Moreover, the hrpG deletion mutant was constructed. To identify the soybean genes responsive to HrpG, two chromosome segment substitution lines (CSSLs) carrying the wild soybean genome, but with opposite phenotypes following Xanthomonas inoculations, were used to analyze gene expression networks based on RNA sequencing at three time points after inoculations with wild-type Xanthomonas or the hrpG deletion mutant. To further identify the hub genes underlying soybean responses to HrpG, the genes located on the substituted chromosome segments were examined. Finally, a combined analysis with the QTLs for resistance to Xanthomonas identified 35 hub genes in the substituted chromosomal segments that may help regulate soybean responses to Xanthomonas and HrpG. Furthermore, two candidate genes in the CSSLs might play pivotal roles in response to Xanthomonas.

Quorum sensing: its role in microbial social networking

Twentieth century observed a huge paradigm shift in the field of sociobiology, which moved from social intelligence of animals to microbes. Quorum Sensing Molecules (QSMs) are the small chemical molecules, which establish the mode of communication among microbes, and is called Quorum Sensing (QS). These molecules are crucial for determining the decisions of large groups of cells, which is a density-dependent process. Thus, this mechanism draws a very thin line between bacteria that are actually prokaryotes and clustered bacteria mimicking eukaryotes. This review discusses about the designs of microbial communication networks, and the role of QS in plant-microbe interaction.

Isolation, characterization and inoculation of Cd tolerant rice endophytes and their impacts on rice under Cd contaminated environment

Cadmium (Cd) contamination in paddy soil becomes increasingly prominent in recent years, which endangers the safe production of food crops. Cd-tolerant endophytes are ideal mediators for decreasing Cd content in rice plants, but their effects on the rice endophytic microbial community and gene expression profile have not yet been well elucidated. In this study, 58 endophytic bacteria from rice seeds were isolated and characterized. Five strains of them were selected based on their potential growth-promoting traits and strong Cd tolerance that could grow well under 4 mM Cd²⁺. By 16S ribosomal RNA (rRNA) identification, these five strains were designated as Enterobacter tabaci R2-7, Pantoea agglomerans R3-3, Stenotrophomonas maltophilia R5-5, Sphingomonas sanguinis R7-3 and Enterobacter tabaci R3-2. Pot experiments in relieving Cd stress in rice plants showed that the S. maltophilia R5-5 performed the strongest potential for reducing the Cd content in root and blade by 81.33% and 77.78%, respectively. The endophytic microbial community diversity, richness and composition were significantly altered in S. maltophilia R5-5 inoculated rice plants. Reverse-transcription qPCR (RT-qPCR) showed that the expression of Cd transporters, OsNramp5 and OsHMA2, were down-regulated in S. maltophilia R5-5-innoculated rice roots. The results indicate that the inoculation of endophytic bacteria S. maltophilia R5-5 provides a reference for alleviating the heavy metal contamination in paddy fields and can be a better alternative for guaranteeing the safe production of crops. Changes in the relative abundance of Cd-resistant microorganisms and the expression of Cd transporters might be the intrinsic factors affecting cadmium content in rice.

Mechanisms of Rice Endophytic Bradyrhizobial Cell Differentiation and Its Role in Nitrogen Fixation

Bradyrhizobium sp. strain SUTN9-2 is a symbiotic and endophytic diazotrophic bacterium found in legume and rice plants and has the potential to promote growth. The present results revealed that SUTN9-2 underwent cell enlargement, increased its DNA content, and efficiently performed nitrogen fixation in response to rice extract. Some factors in rice extract induced the expression of cell cycle and nitrogen fixation genes. According to differentially expressed genes (DEGs) from the transcriptomic analysis, SUTN9-2 was affected by rice extract and the deletion of the bclA gene. The up-regulated DEGs encoding a class of oxidoreductases, which act with oxygen atoms and may have a role in controlling oxygen at an appropriate level for nitrogenase activity, followed by GroESL chaperonins are required for the function of nitrogenase. These results indicate that following its exposure to rice extract, nitrogen fixation by SUTN9-2 is induced by the collective effects of GroESL and oxidoreductases. The expression of the sensitivity to antimicrobial peptides transporter (sapDF) was also up-regulated, resulting in cell differentiation, even when bclA (sapDF) was mutated. This result implies similarities in the production of defensin-like antimicrobial peptides (DEFs) by rice and nodule-specific cysteine-rich (NCR) peptides in legume plants, which affect bacterial cell differentiation.

Monitoring of Rice Transcriptional Responses to Contrasted Colonizing Patterns of Phytobeneficial Burkholderia s.l. Reveals a Temporal Shift in JA Systemic Response

In the context of plant-pathogen and plant-mutualist interactions, the underlying molecular bases associated with host colonization have been extensively studied. However, it is not the case for non-mutualistic beneficial interactions or associative symbiosis with plants. Particularly, little is known about the transcriptional regulations associated with the immune tolerance of plants towards beneficial microbes. In this context, the study of the Burkholderia rice model is very promising to describe the molecular mechanisms involved in associative symbiosis. Indeed, several species of the Burkholderia sensu lato (s.l.) genus can colonize rice tissues and have beneficial effects; particularly, two species have been thoroughly studied: Burkholderia vietnamiensis and Paraburkholderia kururiensis. This study aims to compare the interaction of these species with rice and especially to identify common or specific plant responses. Therefore, we analyzed root colonization of the rice cultivar Nipponbare using DsRed-tagged bacterial strains and produced the transcriptomes of both roots and leaves 7 days after root inoculation. This led us to the identification of a co-expression jasmonic acid (JA)-related network exhibiting opposite regulation in response to the two strains in the leaves of inoculated plants. We then monitored by quantitative polymerase chain reaction (qPCR) the expression of JA-related genes during time course colonization by each strain. Our results reveal a temporal shift in this JA systemic response, which can be related to different colonization strategies of both strains.

Whole genome sequencing and identification of host-interactive genes in the rice endophytic Leifsonia sp. ku-ls

Leifsonia sp. ku-ls is an endophytic bacterial strain colonizing in high numbers the stem and leaf of the high-yielding and widely grown indica rice cultivar RP Bio-226. Whole genome sequencing of this strain using Illumina Hiseq-2500 system resulted in generation of 10,103,994 paired-end reads of 150 nucleotides length. De novo assembly of the reads with A5MySeq resulted in 51 scaffolds. Kmer analysis with KAT estimated the genome size as 3.83 Mbp with 70% GC content. Annotation of the genome resulted in identification of 3930 protein-coding genes, 45 tRNA genes, and 3 rRNA genes. Detailed analysis of the genes predicted resulted in identification of host beneficial genes which include genes associated with hormone production, nitrogen metabolism, and stress response. There is an elaborate defense against oxidative stress present in this bacterium which also can mitigate plant oxidative stress resulting from disease/abiotic stress. Comparison of this endophytic bacterial genome with non-endophytic Leifsonia sp. showed presence of additional genes, increase in copy number of some of the genes and regulators. Many genes with eukaryotic-like domains have also been identified in this bacterium.

Tissue specificity and differential effects on in vitro plant growth of single bacterial endophytes isolated from the roots, leaves and rhizospheric soil of Echinacea purpurea

BACKGROUND

Echinacea-endophyte interaction might affect plant secondary metabolites content and influence bacterial colonization specificity and plant growth, but the underlying mechanisms need deepening. An in vitro model, in which E. purpurea axenic plants as host species and E. angustifolia and Nicotiana tabacum as non-host species inoculated with single endophytes isolated from stem/leaf, root and rhizospheric soil, were used to investigate bacterial colonization.

RESULTS

Colonization analysis showed that bacteria tended to reach tissues from which they were originally isolated (tissue-specificity) in host plants but not in non-host ones (species-specificity). Primary root elongation inhibition as well as the promotion of the growth of E. purpurea and E. angustifolia plants were observed and related to endophyte-produced indole-3-Acetic Acid. Bacteria-secreted substances affected plant physiology probably interacting with plant regulators. Plant metabolites played an important role in controlling the endophyte growth.

CONCLUSIONS

The proposed in vitro infection model could be, generally used to identify novel bioactive compounds and/or to select specific endophytes contributing to the host metabolism properties.

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.

Comparative genomics of Paraburkholderia kururiensis and its potential in bioremediation, biofertilization, and biocontrol of plant pathogens

Burkholderia harbors versatile Gram-negative species and is β-Proteobacteria. Recently, it was proposed to split the genus in two main branches: one of animal and plant pathogens and another, Paraburkholderia, harboring environmental and plant-beneficial species. Currently, Paraburkholderia comprises more than 70 species with ability to occupy very diverse environmental niches. Herein, we sequenced and analyzed the genome of Paraburkholderia kururiensis type strain KP23^T , and compared to P. kururiensis M130, isolated in Brazil, and P. kururiensis susbp. thiooxydans, from Korea. This study focused on the gene content of the three genomes with special emphasis on their potential of plant-association, biocontrol, and bioremediation. The comparative analyses revealed several genes related to plant benefits, including biosynthesis of IAA, ACC deaminase, multiple efflux pumps, dioxygenases, and degradation of aromatic compounds. Importantly, a range of genes for protein secretion systems (type III, IV, V, and VI) were characterized, potentially involved in P. kururiensis well documented ability to establish endophytic association with plants. These findings shed light onto bacteria-plant interaction mechanisms at molecular level, adding novel information that supports their potential application in bioremediation, biofertilization, and biocontrol of plant pathogens. P. kururiensis emerges as a promising model to investigate adaptation mechanisms in different ecological niches.

Sugarcane apoplast fluid modulates the global transcriptional profile of the diazotrophic bacteria Paraburkholderia tropica strain Ppe8

The stalk apoplast fluid of sugarcane contains different sugars, organic acids and amino acids that may supply the demand for carbohydrates by endophytic bacteria including diazotrophs P. tropica (syn. B. tropica) strain Ppe8, isolated from sugarcane, is part of the bacterial consortium recommended as inoculant to sugarcane. However, little information has been accumulated regarding this plant-bacterium interaction considering that it colonizes internal sugarcane tissues. Here, we made use of the RNA-Seq transcriptomic analysis to study the influence of sugarcane stalk apoplast fluid on Ppe8 gene expression. The bacterium was grown in JMV liquid medium (100 ml), divided equally and then supplemented with 50 ml of fresh JMV medium or 50 ml of apoplast fluid extracted from sugarcane variety RB867515. Total RNA was extracted 2 hours later, the rRNAs were depleted and mRNAs used to construct libraries to sequence the fragments using Ion Torrent technology. The mapping and statistical analysis were carried out with CLC Genomics Workbench software. The RNA-seq data was validated by RT-qPCR using the reference genes fliP1, paaF, and groL. The data analysis showed that 544 genes were repressed and 153 genes were induced in the presence of apoplast fluid. Genes that induce plant defense responses, genes related to chemotaxis and movements were repressed in the presence of apoplast fluid, indicating that strain Ppe8 recognizes the apoplast fluid as a plant component. The expression of genes involved in bacterial metabolism was regulated (up and down), suggesting that the metabolism of strain Ppe8 is modulated by the apoplast fluid. These results suggest that Ppe8 alters its gene expression pattern in the presence of apoplast fluid mainly in order to use compounds present in the fluid as well as to avoid the induction of plant defense mechanisms. This is a pioneer study showing the role played by the sugarcane apoplast fluid on the global modulation of genes in P. tropica strain Ppe8.

Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms

A plant microbiome includes a microbial community that typically interacts extensively with a plant. The plant microbiome can survive either inside or outside of plant tissues, performing various plant beneficial activities including biocontrol of potential phytopathogens and promotion of plant growth. An important part of the plant microbiome includes plant growth-promoting bacteria (PGPB) that commonly reside in the rhizosphere and phyllosphere, and as endophytic bacteria (inside of plant tissues). As new plant microbiome-manipulating strategies have emerged in recent years, we have critically reviewed relevant literature, chiefly from the last decade. We have analysed and compared the rhizosphere, phyllosphere and endosphere as potential ecosystems for manipulation, in order to improve positive interactions with the plant. In addition, many studies on the bioengineering of the endophyte microbiome and its potential impact on the core microbiome were analysed with respect to five different strategies, including host mediated and multi-generation microbiome selection, inoculation into soil and rhizosphere, inoculations into seeds or seedlings, tissue atomisation and direct injection into tissues or wounds. Finally, microbiome engineering presents a feasible strategy to solve multiple agriculture-associated problems in an eco-friendly way.

What Is There in Seeds? Vertically Transmitted Endophytic Resources for Sustainable Improvement in Plant Growth

Phytobeneficial microbes, particularly endophytes, such as fungi and bacteria, are concomitant partners of plants throughout its developmental stages, including seed germination, root and stem growth, and fruiting. Endophytic microbes have been identified in plants that grow in a wide array of habitats; however, seed-borne endophytic microbes have not been fully explored yet. Seed-borne endophytes are of great interest because of their vertical transmission; their potential to produce various phytohormones, enzymes, antimicrobial compounds, and other secondary metabolites; and improve plant biomass and yield under biotic and abiotic stresses. This review addresses the current knowledge on endophytes, their ability to produce metabolites, and their influence on plant growth and stress mitigation.

Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria

One of the most exciting scientific advances in recent decades has been the realization that the diverse and immensely active microbial communities are not only 'passengers' with plants, but instead play an important role in plant growth, development and resistance to biotic and abiotic stresses. A picture is emerging where plant roots act as 'gatekeepers' to screen soil bacteria from the rhizosphere and rhizoplane. This typically results in root endophytic microbiome dominated by Proteobacteria, Actinobacteria and to a lesser extent Bacteroidetes and Firmicutes, but Acidobacteria and Gemmatimonadetes being almost depleted. A synthesis of available data suggest that motility, plant cell-wall degradation ability and reactive oxygen species scavenging seem to be crucial traits for successful endophytic colonization and establishment of bacteria. Recent studies provide solid evidence that these bacteria serve host functions such as improving of plant nutrients through acquisition of nutrients from soil and nitrogen fixation in leaves. Additionally, some endophytes can engage 'priming' plants which elicit a faster and stronger plant defense once pathogens attack. Due to these plant growth-promoting effects, endophytic bacteria are being widely explored for their use in the improvement of crop performance. Updating the insights into the mechanism of endophytic bacterial colonization and interactions with plants is an important step in potentially manipulating endophytic bacteria/microbiome for viable strategies to improve agricultural production.

Genomic features of bacterial adaptation to plants

Plants intimately associate with diverse bacteria. Plant-associated (PA) bacteria have ostensibly evolved genes enabling adaptation to the plant environment. However, the identities of such genes are mostly unknown and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots of Brassicaceae, poplar, and maize. We then compared 3837 bacterial genomes to identify thousands of PA gene clusters. Genomes of PA bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant associated genomes. We experimentally validated candidates from two sets of PA genes, one involved in plant colonization, the other serving in microbe-microbe competition between PA bacteria. We also identified 64 PA protein domains that potentially mimic plant domains; some are shared with PA fungi and oomycetes. This work expands the genome-based understanding of plant-microbe interactions and provides leads for efficient and sustainable agriculture through microbiome engineering.

Diversity of nodular bacteria ofScorpiurus muricatusin western Algeria and their impact on plant growth

A total of 51 bacterial strains were isolated from root nodules of Scorpiurus muricatus sampled from 6 regions of western Algeria. Strain diversity was assessed by rep-PCR amplification fingerprinting, which grouped the isolates into 28 different clusters. Partial nucleotide sequencing of the 16S rRNA gene and BLAST analysis revealed that root nodules of S. muricatus were colonized by different species close to Rhizobium vignae, Rhizobium radiobacter, Rhizobium leguminosarum, Phyllobacterium ifriqiyense, Phyllobacterium endophyticum, Starkeya sp., and Pseudomonas sp. However, none of these strains was able to form nodules on its host plant; even nodC was present in a single strain (SMT8a). The inoculation test showed a great improvement in the growth of inoculated plants compared with noninoculated control plants. A significant amount of indole acetic acid was produced by some strains, but only 2 strains could solubilize phosphate. In this report we described for the first time the diversity of bacteria isolated from root nodules of S. muricatus growing in different regions in western Algeria and demonstrated their potential use in promoting plant growth.

Shoot the Message, Not the Messenger-Combating Pathogenic Virulence in Plants by Inhibiting Quorum Sensing Mediated Signaling Molecules

Immunity, virulence, biofilm formation, and survival in the host environment are regulated by the versatile nature of density dependent microbial cell signaling, also called quorum sensing (QS). The QS molecules can associate with host plant tissues and, at times, cause a change in its gene expression at the downstream level through inter-kingdom cross talking. Progress in controlling QS through fungicide/bactericide in pathogenic microscopic organisms has lead to a rise of antibiotic resistance pathogens. Here, we review the application of selective quorum quenching (QQ) endophytes to control phytopathogens that are shared by most, if not all, terrestrial plant species as well as aquatic plants. Allowing the plants to posses endophytic colonies through biotization will be an additional and a sustainable encompassing methodology resulting in attenuated virulence rather than killing the pathogens. Furthermore, the introduced endophytes could serve as a potential biofertilizer and bioprotection agent, which in turn increases the PAMP- triggered immunity and hormonal systemic acquired resistance (SAR) in plants through SA-JA-ET signaling systems. This paper discusses major challenges imposed by QS and QQ application in biotechnology.

Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria

One of the most exciting scientific advances in recent decades has been the realization that the diverse and immensely active microbial communities are not only 'passengers' with plants, but instead play an important role in plant growth, development and resistance to biotic and abiotic stresses. A picture is emerging where plant roots act as 'gatekeepers' to screen soil bacteria from the rhizosphere and rhizoplane. This typically results in root endophytic microbiome dominated by Proteobacteria, Actinobacteria and to a lesser extent Bacteroidetes and Firmicutes, but Acidobacteria and Gemmatimonadetes being almost depleted. A synthesis of available data suggest that motility, plant cell-wall degradation ability and reactive oxygen species scavenging seem to be crucial traits for successful endophytic colonization and establishment of bacteria. Recent studies provide solid evidence that these bacteria serve host functions such as improving of plant nutrients through acquisition of nutrients from soil and nitrogen fixation in leaves. Additionally, some endophytes can engage 'priming' plants which elicit a faster and stronger plant defense once pathogens attack. Due to these plant growth-promoting effects, endophytic bacteria are being widely explored for their use in the improvement of crop performance. Updating the insights into the mechanism of endophytic bacterial colonization and interactions with plants is an important step in potentially manipulating endophytic bacteria/microbiome for viable strategies to improve agricultural production.

Biological Control of Rice Bakanae by an Endophytic Bacillus oryzicola YC7007

In our previous study, we reported that a novel endophytic bacterium Bacillus oryzicola YC7007 has suppressed bacterial diseases of rice via induced systemic resistance and antibiotic production. This endophytic strain, B. oryzicola YC7007 was used as a biological control agent against bakanae disease of rice caused by Fusarium fujikuroi, and its mechanism of interaction with the pathogen and the rice was further elucidated. Root drenching with B. oryzicola YC7007 suspension reduced the disease severity of bakanae significantly when compared with the untreated controls. The treatments of B. oryzicola YC7007 suspension (2.0 × 10(7) cfu/ml) to the rice rhizosphere reduced bakanae severity by 46-78% in pots and nursery box tests containing autoclaved and non-autoclaved soils. Moreover, in the detached rice leaves bioassay, the development of necrotic lesion and mycelial expansion of F. fujikuroi were inhibited significantly by spraying the culture filtrate of B. oryzicola YC7007. Drenching of ethyl acetate extracts of the culture filtrate to the rhizosphere of rice seedlings also reduced the bakanae disease severity in the plant culture dish tests. With the root drenching of B. oryzicola YC7007 suspension, the accumulation of hydrogen peroxide was observed at an early stage of rice seedlings, and a hormonal defense was elicited with and without pathogen inoculation. Our results showed that the strain B. oryzicola YC7007 had a good biocontrol activity against the bakanae disease of rice by direct inhibition, and was also capable of inducing systemic resistance against the pathogen via primed induction of the jasmonic acid pathway.