Native bacterial endophytes promote host growth in a species-specific manner; phytohormone manipulations do not result in common growth responses

Phyllosphere fungal diversity generates pervasive nonadditive effects on plant performance

Plants naturally harbor diverse microbiomes that can dramatically impact their health and productivity. However, it remains unclear how fungal microbiome diversity, especially in the phyllosphere, impacts intermicrobial interactions and consequent nonadditive effects on plant productivity. Combining manipulative experiments, field collections, culturing, microbiome sequencing, and synthetic consortia, we experimentally tested for the first time how foliar fungal community diversity impacts plant productivity. We inoculated morning glories (Ipomoea hederifolia L.) with 32 phyllosphere consortia of either low or high diversity or with single fungal taxa, and measured effects on plant productivity and allocation. We found the following: (1) nonadditive effects were pervasive with 56% of fungal consortia interacting synergistically or antagonistically to impact plant productivity, including some consortia capable of generating acute synergism (e.g. > 1000% increase in productivity above the additive expectation), (2) interactions among 'commensal' fungi were responsible for this nonadditivity in diverse consortia, (3) synergistic interactions were approximately four times stronger than antagonistic effects, (4) fungal diversity affected the magnitude but not frequency or direction of nonadditivity, and (5) diversity affected plant performance nonlinearly with the highest performance in low-diversity treatments. These findings highlight the importance of interpreting plant-microbiome interactions under a framework that incorporates intermicrobial interactions and nonadditive outcomes to understand natural complexity.

Up-regulation of growth-related gene expression in tobacco by volatile compounds released by Bacillus velezensis WSW007

In order to investigate the mechanism of plant growth promoting (PGP) effects of strain Bacillus velezensis WSW007, its PGP traits and production of volatile organic compounds (VOCs) were tested. The effects of VOCs produced by strain WSW007 on plant growth were observed by co-culturing this strain with tobacco seedlings in I-plates. Meanwhile, the effects of VOCs on tobacco gene expression were analysed by a transcriptome analysis and VOCs were identified by solid phase micro extraction coupled with gas chromatography-mass spectrometry (SPME-GC-MS) analysis. As results, strains WSW007 produced acetic acid and siderophore, and could solubilize phosphate; while it also significantly increased the fresh weight of tobacco seedlings via production of VOCs. In transcriptome analysis, plants co-cultured with strain WSW007 presented the highest up-regulated expression for the genes involved in plant growth and development processes, implying that the bacterial VOCs played a role as regulator of plant gene expression. Conclusively, the up-regulation in expression of growth- and development-related genes via VOCs production is an important PGP mechanism in strain B. velezensis WSW007.

Invisible Inhabitants of Plants and a Sustainable Planet: Diversity of Bacterial Endophytes and their Potential in Sustainable Agriculture

Uncontrolled usage of chemical fertilizers, climate change due to global warming, and the ever-increasing demand for food have necessitated sustainable agricultural practices. Removal of ever-increasing environmental pollutants, treatment of life-threatening diseases, and control of drug-resistant pathogens are also the need of the present time to maintain the health and hygiene of nature, as well as human beings. Research on plant-microbe interactions is paving the way to ameliorate all these sustainably. Diverse bacterial endophytes inhabiting the internal tissues of different parts of the plants promote the growth and development of their hosts by different mechanisms, such as through nutrient acquisition, phytohormone production and modulation, protection from biotic or abiotic challenges, assisting in flowering and root development, etc. Notwithstanding, efficient exploitation of endophytes in human welfare is hindered due to scarce knowledge of the molecular aspects of their interactions, community dynamics, in-planta activities, and their actual functional potential. Modern "-omics-based" technologies and genetic manipulation tools have empowered scientists to explore the diversity, dynamics, roles, and functional potential of endophytes, ultimately empowering humans to better use them in sustainable agricultural practices, especially in future harsh environmental conditions. In this review, we have discussed the diversity of bacterial endophytes, factors (biotic as well as abiotic) affecting their diversity, and their various plant growth-promoting activities. Recent developments and technological advancements for future research, such as "-omics-based" technologies, genetic engineering, genome editing, and genome engineering tools, targeting optimal utilization of the endophytes in sustainable agricultural practices, or other purposes, have also been discussed.

Unraveling the functional characteristics of endophytic bacterial diversity for plant growth promotion and enhanced secondary metabolite production in Pelargonium graveolens

The rich diversity of microbial endophytic communities associated with plants, often referred to as the second genome, serves as a compelling illustration of efficient co-evolution. This noteworthy partnership plays a pivotal role in sustaining plant well-being and enhancing plant adaptability across diverse habitats. Therefore, examining the diversity of endophytic microbes associated with their particular host plant is valuable for gaining insights into the vast spectrum of plant-microbe interactions. The present experiments aimed at investigating the bacterial endophytic diversity in both root and shoot tissues of Pelargonium graveolens, employing culture dependent and culture independent high-throughput metagenomics approach. A total of 614 and 620 operational taxonomic units (OTUs), encompassing 291 and 229 genera, were identified in the shoot and root tissues of P. graveolens, respectively. Furthermore, the subsequent classification of OTUs revealed 15 highly abundant phyla, with Proteobacteria dominating both root and shoot tissues. Notably, an exceptionally high abundance of Firmicutes phyla was observed in the shoot compared to the root. Additionally, 30 bacterial endophytes from the root, stem, petiole, and leaves were isolated and molecularly characterized, unveiling a consistent pattern of diversity distribution between the root and shoot of P. graveolens. Upon screening all isolates for plant growth promoting traits, Pseudomonas oryzihabitans was found to be positive for major biochemical test like nitrogen fixation, phosphate solubilization etc. and on inoculation resulted in about two-fold increase in content of essential oil accompanied by a significant rise in the geraniol and citronellol content. Diving deep into the genetic constitution of P. oryzihabitans unveiled a substantial number of genes directly and indirectly contributing to the endophyte's capability in colonizing host plants effectively. In summary, data obtained from metagenomics and culture dependent approaches including glass house trials suggest potential bacterial endophytes suitable for field applications for yield enhancement and in planta secondary metabolite enhancement investigations.

An updated view of bacterial endophytes as antimicrobial agents against plant and human pathogens

Bacterial endophytes are a crucial component of the phytomicrobiome, playing an essential role in agriculture and industries. Endophytes are a rich source of bioactive compounds, serving as natural antibiotics that can be effective in combating antibiotic resistance in pathogens. These bacteria interact with host plants through various processes such as quorum sensing, chemotaxis, antibiosis, and enzymatic activity. The current paper focuses on how plants benefit extensively from endophytic bacteria and their symbiotic relationship in which the microbes enhance plant growth, nitrogen fixation, increase nutrient uptake, improve defense mechanisms, and act as antimicrobial agents against pathogens. Moreover, it highlights some of the bioactive compounds produced by endophytes.

Carbon nanosol-induced assemblage of a plant-beneficial microbiome consortium

Carbon nanosol (CNS) is a carbon-based nanomaterial that promotes plant growth; however, its functional mechanisms and effects on the microbiome are not fully understood. Here, we explored the effects of CNS on the relationship between the soil, endophytic microbiomes and plant productivity. CNS treatment increased the fresh biomass of tobacco (Nicotiana tabacum L.) plants by 27.4% ± 9.9%. Amplicon sequencing analysis showed that the CNS treatment significantly affected the composition and diversity of the microbial communities in multiple ecological niches associated with tobacco, especially the bulk soil and stem endophytic microbiome. Furthermore, the application of CNS resulted in enhanced network connectivity and stability of the microbial communities in different niches, particularly in the soil, implying a strengthening of certain microbial interactions. Certain potentially growth-promoting root endophytic bacteria were more abundant under the CNS treatment. In addition, CNS increased the abundance of some endophytic microbial functional genes known to enhance plant growth, such as those associated with nutrient metabolism and the plant hormone biosynthesis pathways. We isolated two bacterial strains (Sphingopyxis sp. and Novosphingobium sp.) that were enriched under CNS treatment, and they were confirmed to promote tobacco plant growth in vitro. These results suggested that CNS might, at least in part, promote plant growth by enriching beneficial bacteria in the microbiome.

Plant-soil feedback under drought: does history shape the future?

Plant-soil feedback (PSF) is widely recognised as a driver of plant community composition, but understanding of its response to drought remains in its infancy. Here, we provide a conceptual framework for the role of drought in PSF, considering plant traits, drought severity, and historical precipitation over ecological and evolutionary timescales. Comparing experimental studies where plants and microbes do or do not share a drought history (through co-sourcing or conditioning), we hypothesise that plants and microbes with a shared drought history experience more positive PSF under subsequent drought. To reflect real-world responses to drought, future studies need to explicitly include plant-microbial co-occurrence and potential co-adaptation and consider the precipitation history experienced by both plants and microbes.

Bioinoculant mediated regulation of signalling cascades in various stress responses in plants

Bio-inoculation involves the association of plant with some beneficial microorganisms, and among these microbiotas, those bacteria which can promote plant growth and development are known as Plant Growth Promoting Rhizobacteria (PGPR). It can help a plant directly or indirectly, which includes root development, biological nitrogen (N₂) fixation, stress tolerance, cell division and elongation, solubilization of Zinc, Phosphate, Potassium, soil health improvement and many more. PGPR have gained attention as it can be used as biofertilizers and helpful in bioremediation techniques, which in turn can reduce the chemical dependency in agriculture. PGPR mediated plant growth and stress management is developed by the virtue of the interaction of plant and microbial signalling pathways. On the other hand, environmental stresses are something to which a plant is always exposed irrespective of other factors. The present review is all about the better understanding of the convergence strategies of these signalling molecules and the ambiguities of signalling activities occurring in the host due to the interaction with PGPR under environmental stressed conditions.

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.

Evaluation of inorganic phosphate solubilizing efficiency and multiple plant growth promoting properties of endophytic bacteria isolated from root nodules Erythrina brucei

Background

In soils, phosphorous (P) mostly exists in fixed/insoluble form and unavailable for plants use in soil solution, hence it is in scarcity. P is fixed in the form of aluminium, iron and manganese phosphates in acidic soils and calcium phosphate in alkaline soils. Phosphate solubilizing bacteria, the ecological engineers play a pivotal role in the mobilization of fixed forms of P by using different mechanisms. The objectives of this study were to evaluate inorganic phosphate solubilizing efficiency and other multiple plant growth promoting traits of Erythrina brucei root nodule endophytic bacteria and to investigate effects of the selected endophytic bacteria on the growth of wheat plant under phosphorous deficient sand culture at greenhouse conditions.

Results

Among a total of 304 passenger endophytic bacteria, 119 (39%) exhibited tricalcium phosphate (TCP) solubilization; however, none of them were formed clear halos on solid medium supplemented with aluminum phosphate (Al-P) or iron phosphate (Fe–P). Among 119 isolates, 40% exhibited IAA production. The selected nine potential isolates also exhibited potentials of IAA, HCN, NH₃ and/or hydrolytic enzymes production. All the selected isolates were potential solubilizers of the three inorganic phosphates (Al-P, Fe–P and TCP) included in liquid medium. The highest values of solubilized TCP were recorded by isolates AU4 and RG6 (A. soli), 108.96 mg L⁻¹ and 107.48 mg L⁻¹, respectively at sampling day3 and 120.36 mg L⁻¹ and 112.82 mg L⁻¹, respectively at day 6. The highest values of solubilized Al-P and Fe–P were recorded by isolate RG6, 102.14 mg L⁻¹ and 96.07 mg L⁻¹, respectively at sampling days 3 and 6, respectively. The highest IAA, 313.61 µg mL⁻¹ was recorded by isolate DM17 (Bacillus thuringiensis). Inoculation of wheat with AU4, RG6 and RG5 (Acinetobacter soli) increased shoot length by 11, 17.4 and 14.6%, respectively compared to the negative control. Similarly, 76.9, 69.2 and 53.8% increment in shoot dry weight is recorded by inoculation with RG6, AU4 and RG5, respectively. These nine potential endophytic isolates are identified to Gluconobacter cerinus (4), Acinetobacter soli (3), Achromobacter xylosoxidans (1) and Bacillus thuringiensis (1).

Conclusion

AU4, RG6 and RG5 can be potential bio-inoculants candidates as low cost agricultural inputs in acidic and/or alkaline soils for sustainable crop production.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02688-7.

Root-Associated Bacteria Community Characteristics of Antarctic Plants: Deschampsia antarctica and Colobanthus quitensis-a Comparison

Colobanthus quitensis (Kunth) Bartl. and Deschampsia antarctica Desv. are the only Magnoliophyta to naturally colonize the Antarctic region. The reason for their sole presence in Antarctica is still debated as there is no definitive consensus on how only two unrelated flowering plants managed to establish breeding populations in this part of the world. In this study, we have explored and compared the rhizosphere and root-endosphere dwelling microbial community of C. quitensis and D. antarctica specimens sampled in maritime Antarctica from sites displaying contrasting edaphic characteristics. Bacterial phylogenetic diversity (high-throughput 16S rRNA gene fragment targeted sequencing) and microbial metabolic activity (Biolog EcoPlates) with a geochemical soil background were assessed. Gathered data showed that the microbiome of C. quitensis root system was mostly site-dependent, displaying different characteristics in each of the examined locations. This plant tolerated an active bacterial community only in severe conditions (salt stress and nutrient deprivation), while in other more favorable circumstances, it restricted microbial activity, with a possibility of microbivory-based nutrient acquisition. The microbial communities of D. antarctica showed a high degree of similarity between samples within a particular rhizocompartment. The grass' endosphere was significantly enriched in plant beneficial taxa of the family Rhizobiaceae, which displayed obligatory endophyte characteristics, suggesting that at least part of this community is transmitted vertically. Ultimately, the ecological success of C. quitensis and D. antarctica in Antarctica might be largely attributed to their associations and management of root-associated microbiota.

Potential of plant growth promoting bacterial consortium for improving the growth and yield of wheat under saline conditions

Owing to inconsistent results of a single bacterial strain, co-inoculation of more than one strain under salinity stress could be a more effective strategy to induce salt tolerance. Co-inoculation of more than one bacterial strain could be more effective due to the presence of several growths promoting traits. This study was conducted to evaluate the effectiveness of multi-strains bacterial consortium to promote wheat growth under salinity stress. Several plant growth promoting rhizobacteria (PGPR) had been isolated and tested for their ability to grow in increasing concentrations of sodium chloride (NaCl). Those rhizobacterial strains having tolerance against salinity were screened to evaluate their ability to promote wheat growth in the presence of salinity by conducting jar trials under axenic conditions. The rhizobacteria with promising results were tested for their compatibility with each other before developing multi-strain inoculum of PGPR. The compatible PGPR strains were characterized, and multi-strain inoculum was then evaluated for promoting wheat growth under axenic conditions at different salinity levels, i.e., 2.1 (normal soil), 6, 12, and 18 dS m^–1. The most promising combination was further evaluated by conducting a pot trial in the greenhouse. The results showed that compared to a single rhizobacterial strain, better growth-promoting effect was observed when rhizobacterial strains were co-inoculated. The multi-strain consortium of PGPR caused a significant positive impact on shoot length, root length, shoot fresh weight, and root fresh weight of wheat at the highest salinity level in the jar as well as in the pot trial. Results showed that the multi-strain consortium of PGPR caused significant positive effects on the biochemical traits of wheat by decreasing electrolyte leakage and increasing chlorophyll contents, relative water contents (RWC), and K/Na ratio. It can be concluded that a multi-strain consortium of PGPR (Ensifer adhaerens strain BK-30, Pseudomonas fluorescens strain SN5, and Bacillus megaterium strain SN15) could be more effective to combat the salinity stress owing to the presence of a variety of growth-promoting traits. However, further work is going on to evaluate the efficacy of multi-strain inoculum of PGPR under salt-affected field conditions.

Genotype-Specific Plastic Responses to Seed Bacteria under Drought Stress in Lactuca serriola

Recent studies have demonstrated that seed-borne bacteria can enhance the performance of invasive plants in novel introduced habitats with environmental stresses. The effect of this plant-bacteria interaction may vary with plant species or even genotype; however, the genotype-dependent effects of seed bacteria have rarely been assessed. In this study, we examined the effects of bacterial strains isolated from seeds on the genotypes of an invasive xerophytic plant, Lactuca serriola. Plant genotypes were grown under drought conditions, and their plastic responses to bacterial infections were evaluated. Some genotypes produced more biomass, whereas others produced less biomass in response to infection with the same bacterial strain. Notably, the quantity of root-adhering soil depended on the bacterial treatment and plant genotypes and was positively correlated with the plastic responses of plant performance. Because tested bacteria could colonize the plant rhizosphere, bacterial infection appears to induce the differential formation of soil rhizosheaths among plant genotypes, consequently affecting the maintenance of soil water content under drought conditions. Given that drought tolerance is a critical attribute for the invasive success of L. serriola, these results imply that bacterial symbionts can facilitate the establishment of alien plant species, but their effects are likely genotype-specific.

Seed-Derived Microbial Community of Wild Cicer Seedlings: Composition and Augmentation to Domesticated Cicer

Seed-borne bacteria are a unique group of microorganisms capable of maintaining stable populations within plant tissues and seeds. These bacteria may benefit their host from germination to maturation and are of great interest for basic and applied plant-microbe interaction studies. Furthermore, many such beneficial bacteria present in wild plant species are missing in their respective congeneric domesticated forms. The objectives of this study were to explore the bacterial communities within the seeds of wild Cicer species and to select beneficial bacteria which could be used to improve production of domesticated chickpea (C. arietinum). We analyzed the composition of seed-borne bacteria of chickpea (Cicer spp.), comparing wild and domesticated species from different geographic locations. Subsequently, we isolated the dominant and prevalent seed-borne bacteria from wild Cicer judaicum and assessed their ability to colonize and affect the growth of domesticated chickpea and other legume crops. The composition and structure of seed-borne bacteria, determined by amplicon sequencing of the 16S rRNA gene, differed between wild and domesticated chickpea and varied among geographic locations. The genus Burkholderia dominated samples from domesticated chickpea at all examined sites, while Bacillus or Sphingomonas dominated cultures isolated from wild C. judaicum, dependent on geographic location. A particular Bacillus strain, Bacillus sp. CJ, representing the most prevalent bacterium in wild C. judaicum, was further isolated. Bacillus sp. CJ, applied by seed coating, successfully inhabited domesticated chickpea plants and improved plant growth parameters. These results demonstrate the potential for reconstructing the microbiota of crop plants using the wild microbiota reservoir. IMPORTANCE Chickpea (garbanzo bean, hummus, Cicer arietinum) representing the third legume crop produced globally. As is the case for many other domesticated crops, the adaptation and resistance of chickpea to biotic and abiotic stresses is inferior compared to that of their wild progenitors and relatives. Re-establishing desirable characteristics from wild to domesticated species may be achieved by reconstructing beneficial microbiota. In this study, we examined the seed-associated microbiota of both wild and domesticated chickpea and applied isolated beneficial bacteria originating from wild Cicer judaicum to domesticated chickpea by seed coating. This isolate, Bacillus sp. CJ, was successfully established in the crop and enhanced its growth, demonstrating effective and efficient manipulation of the chickpea microbiota as a potential model for future application in other crop plants.

Wheat grain proteomic and protein-metabolite interactions analyses provide insights into plant growth promoting bacteria-arbuscular mycorrhizal fungi-wheat interactions

Proteomic, protein-protein and protein-metabolite interaction analyses in wheat inoculated with PGPB and AMF identified key proteins and metabolites that may have a role in enhancing yield and biofortification. Plant growth-promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF) have an impact on grain yield and nutrition. This dynamic yet complex interaction implies a broad reprogramming of the plant's metabolic and proteomic activities. However, little information is available regarding the role of native PGPB and AMF and how they affect the plant proteome, especially under field conditions. Here, proteomic, protein-protein and protein-metabolite interaction studies in wheat triggered by PGPB, Bacillus subtilis CP4 either alone or together with AMF under field conditions was carried out. The dual inoculation with native PGPB (CP4) and AMF promoted the differential abundance of many proteins, such as histones, glutenin, avenin and ATP synthase compared to the control and single inoculation. Interaction study of these differentially expressed proteins using STRING revealed that they interact with other proteins involved in seed development and abiotic stress tolerance. Furthermore, these interacting proteins are involved in carbon fixation, sugar metabolism and biosynthesis of amino acids. Molecular docking predicted that wheat seed storage proteins, avenin and glutenin interact with secondary metabolites, such as trehalose, and sugars, such as xylitol. Mapping of differentially expressed proteins to KEGG pathways showed their involvement in sugar metabolism, biosynthesis of secondary metabolites and modulation of histones. These proteins and metabolites can serve as markers for improving wheat-PGPB-AMF interactions leading to higher yield and biofortification.

Plant growth-promoting rhizobacteria Shewanella putrefaciens and Cronobacter dublinensis enhance drought tolerance of pearl millet by modulating hormones and stress-responsive genes

Drought is a major abiotic stress that affects crop productivity. Endophytic bacteria have been found to alleviate the adverse effects of drought on plants. In the present study, we evaluated the effects of two endophytic bacteria Shewanella putrefaciens strain MCL-1 and Cronobacter dublinensis strain MKS-1 on pearl millet (Pennisetum glaucum (L.) R. Br.) under drought stress conditions. Pearl millet plants were grown under three water levels: field capacity (FC), mild drought stress (MD), and severe drought stress (SD). The effects of inoculation on plant growth, physiological attributes, phytohormone content, and drought stress-responsive genes were assessed. The inoculation of pearl millet seeds with endophytes significantly improved shoot and root dry weight and root architecture of plants grown under FC and drought stress conditions. There was a significant increase in relative water content and proline accumulation in the inoculated plants. Among the phytohormones analyzed, the content of ABA and IAA was significantly higher in endophyte-treated plants under all moisture regimes than in uninoculated plants. C. dublinensis-inoculated plants had higher GA content than uninoculated plants under all moisture regimes. The expression level of genes involved in phytohormone biosynthesis (SbNCED, SbGA20oX, and SbYUC) and coding drought-responsive transcription factors (SbAP2, SbSNAC1 and PgDREB2A) was significantly higher under SD in endophyte-inoculated plants than in uninoculated plants. Thus, these endophytic bacteria presumably enhanced the tolerance of pearl millet to drought stress by modulating root growth, plant hormones, physiology and the expression of genes involved in drought tolerance.

Variation of the seed endophytic bacteria among plant populations and their plant growth-promoting activities in a wild mustard plant species, Capsella bursa-pastoris

Recent studies have revealed that some bacteria can inhabit plant seeds, and they are likely founders of the bacterial community in the rhizosphere of or inside plants at the early developmental stage. Given that the seedling establishment is a critical fitness component of weedy plant species, the effects of seed endophytic bacteria (SEB) on the seedling performance are of particular interest in weed ecology. Here, we characterized the SEB in natural populations of Capsella bursa-pastoris, a model species of weed ecology. The composition of endophytic bacterial community was evaluated using deep sequencing of a 16S rDNA gene fragment. Additionally, we isolated bacterial strains from seeds and examined their plant growth-promoting traits. Actinobacteria, Firmicutes, Alpha-, and Gammaproteobacteria were major bacterial phyla inside seeds. C. bursa-pastoris natural populations exhibited variable seed microbiome such that the proportion of Actinobacteria and Alphaproteobacteria differed among populations, and 60 out of 82 OTUs occurred only in a single population. Thirteen cultivable bacterial species in six genera (Bacillus, Rhodococcus, Streptomyces, Staphylococcus, Paenibacillus, Pseudomonas) were isolated, and none of them except Staphylococcus haemolyticus were previously reported as seed endophytes. Eight isolates exhibited plant growth-promoting traits like phosphate solubilization activity, indole-3-acetic acid, or siderophore production. Despite the differences in the bacterial communities among plant populations, at least one isolated strain from each population stimulated shoot growth of either C. bursa-pastoris or its close relative A. thaliana when grown with plants in the same media. These results suggest that a weedy plant species, C. bursa-pastoris, contains bacterial endophytes inside their seeds, stimulating seedling growth and thereby potentially affecting seedling establishment.

Interaction among endophytic bacteria, sweet sorghum (Sorghum bicolor) cultivars and chemical nitrogen fertilization

The application of new agricultural technologies to attain sustainable production systems is necessary. The use of plant growth-promoting bacteria to improve plant growth and health has been studied for decades. This work aimed to isolate diazotrophic endophytic bacteria associated with sweet sorghum plants and study the interaction of their inoculation in combination with chemical N-fertilization on different sorghum cultivars. A bacterial collection of 181 isolates was constructed and characterized in vitro and in vivo. From that, the strains Enterobacter sp. UYSB89 and Kosakonia sp. UYSB139 were nifH+, produce IAA, defined as true endophytes and able to promote growth of two sweet sorghum under greenhouse conditions. The evaluated cultivars responded differentially to bacterial inoculation, the nitrogen fertilization doses and their interaction. Thus, plant growth is a multifactorial consequence of the interrelation between crop practices and the plant genotypes. This knowledge is a valuable factor in terms of understanding plant-bacteria endophyte interactions to preserve environmental sustainability during the implementation of agronomic practices.

Alleviation of Submergence Stress in Rice Seedlings by Plant Growth-Promoting Rhizobacteria With ACC Deaminase Activity

Submergence stress slows seed germination, imposes fatalities, and delays seedling establishment in rice. Seeds of submergence susceptible rice variety IR 42 were inoculated with four 1-aminocyclopropane-1-carboxylic acid (ACC) utilizing isolates viz., Bacillus sp. (AR-ACC1), Microbacterium sp. (AR-ACC2), Methylophaga sp. (AR-ACC3), and Paenibacillus sp. (ANR-ACC3) and subjected to submergence stress under controlled conditions for 7 days. Seeds treated with Microbacterium sp. AR-ACC2, Paenibacillus sp. ANR-ACC3, and Methylophaga sp. AR-ACC3 significantly enhanced the germination percentage (GP), seedling vigor index (SVI), and other growth parameters like root and shoot length and total chlorophyll contents, when compared with nonbacterized seeds submerged similarly. However, the values were statistically at par when control seeds were treated with l-α-(2-aminoethoxyvinyl) glycine hydrochloride (AVG), a known inhibitor of ethylene production. Results suggest that stress ethylene production was significantly reduced by around 85% in seedlings treated with Microbacterium sp. AR-ACC2 as compared with untreated control seeds under submergence. Paenibacillus sp. ANR-ACC3 and Methylophaga sp. AR-ACC3 were the next effective strains. Ethylene synthesis in seedlings was statistically at par with seeds treated with AVG suggesting ACC deaminase can effectively reduce ethylene levels in plants subjected to submergence. Bacillus sp. (AR-ACC1) was neither able to significantly promote seedling growth parameters nor inhibit ethylene production as compared with control seeds. Results suggest that flooded soil planted to rice harbor microorganisms with plant growth-promoting properties that can be used effectively to alleviate submergence stresses in susceptible rice varieties under field conditions.

Comparative assessment of multi-trait plant growth-promoting endophytes associated with cultivated and wild Oryza germplasm of Assam, India

This paper presents a comparative study of endophytic bacteria from cultivated (Oryza sativa) and wild rice (Oryza rufipogon) plants and their functional traits related to plant growth promotion. A total of 70 bacterial isolates were characterized by both biochemical and molecular identification methods. Taxonomic classification showed dominance of three major phyla, viz, Firmicutes (57.1%), Actinobacteria (20.0%) and Proteobacteria (22.8%). Screening for in vitro plant growth-promoting activities revealed a hitherto unreported endophytic bacterium from wild rice germplasm, Microbacterium laevaniformans RS0111 with highest indole acetic acid (28.39 ± 1.39 µg/ml) and gibberellic acid (67.23 ± 1.83 µg/ml) producing efficiency. Few other endophytic isolates from cultivated rice germplasm such as Bacillus tequilensis RHS01 showed highest phosphate solubilizing activity (81.70 ± 1.98 µg/ml), while Microbacterium testaceum MKLS01 and Microbacterium enclense MI03 L05 showed highest potassium (53.42 ± 0.75 µg/ml) and zinc solubilizing activity (157.50%). Fictibacillus aquaticus LP20 05 produced highest siderophore (64.8%). In vivo evaluation of plant growth-promoting efficiencies of the isolates showed that Microbacterium laevaniformans RS0111, Microbacterium testaceum MKLS01 and Bacillus tequilensis RHS 01 could increase rice grain yield by 3.4-fold when compared to the control group. This study indicates the potentiality of rice endophytes isolates as an effective bioinoculants.

Comprehensive assessment of growth parameters for screening endophytic bacterial strains in Solanum lycopersicum (Tomato)

Conventional agricultural practices demand application of pesticides for better yield, yet their uncontrolled use for longer duration exhibit deleterious effects on the soil health and subsequent plant productivity. These circumstances have displayed alarming effects on food security in the modern world. Therefore, biological solutions to the crisis can be practiced in consideration to their environmental benefits. Bacterial endophytes are ubiquitous in the phytosystem and beneficial for the plant growth and productivity. The present study aimed to obtain endophytic bacterial strains that can be developed as effective plant growth promoters. For this purpose twelve strains of bacterial endophytes were isolated from different plant sources and their putative plant growth promoting attributes were analyzed by morphological and biochemical studies. Subsequently these isolates were inoculated in the Solanum lycopersicum (Tomato) and the factors like germination percentage, seedling length, biomass production, and leaf variables were analyzed. However, the vigour index was considered as the prime parameter for determining plant growth. In essence, RR2 and RR4 strains were observed as effective growth promoter, hence in future they can be utilized as effective biofertilizers.

Diversity of bacterial endophyte in Eucalyptus clones and their implications in water stress tolerance

The genus Eucalyptus with over 747 species occurs in wide ecological range and is preferred for bioenergy plantations due to their short rotation, rapid growth and superior wood properties. They are planted in 22 million ha area and India is third largest planter of Eucalyptus. In the present study, the bacterial endophyte community in leaves of six Eucalyptus clones belonging to E. tereticornis and E. camaldulensis was assessed by sequencing the V3-V4 region of the bacterial 16S rRNA gene. The clones were selected based on their response to progressive water stress. A total of 4947 operational taxonomic units (OTUs) were obtained and the dominant phyla were Proteobacteria, Bacteroidetes and Firmicutes. Escherichia coli was enriched in all samples at species level. Comparison of endophyte diversity was conducted between the two species and across the water stress tolerant and susceptible clones. The alpha-diversity analysis revealed that species richness and diversity was high in E. camaldulensis and water stress susceptible clones. LefSe analysis predicted 69 and 54 significantly enriched taxonomic biomarkers between species and stress response groups respectively. A maximum of 49 taxonomic biomarkers were recorded in susceptible group and the significantly enriched species were Bacteroides thetaiotaomicron and Turicibacter sanguinis, while the tolerant group documented 5 biomarkers including oscillibacter sp. The presence of functional biomarkers was also assessed in both the groups. The findings of the present study provides an insight into the diversity of bacterial endophyte in Eucalyptus leaves and to our knowledge this is the first report on documenting the endophyte abundance in water stress responsive Eucalyptus clones.

The Response of Maize to Inoculation with Arthrobacter sp. and Bacillus sp. in Phosphorus-Deficient, Salinity-Affected Soil

Salinity and phosphorus (P) deficiency are among the most serious soil factors constraining crop productivity. A proposed strategy for alleviating these stresses is supporting plants by inoculation with growth-promoting rhizobacteria (PGPR). Here, a comparison of the ability of two maize composite and two F1 hybrid varieties to tolerate a P deficiency in either a saline or a non-saline environment showed that the uptake of nutrients by all four entries was significantly reduced by the imposition of both soil salinity and P deficiency, and that their growth was compromised to a similar extent. Subsequently, the ameliorative effect of inoculation with three strains of either Arthrobacter sp. or Bacillus sp. in an environment, which suffered simultaneously from salinity and P deficiency, was investigated. Inoculation with each of the strains was found to limit the plants’ uptake of sodium cations, to increase their uptake of potassium cations, and to enhance their growth. The extent of the growth stimulation was more pronounced for the composite varieties than for the F1 hybrid ones, although the amount of biomass accumulated by the latter, whether the plants had been inoculated or not, was greater than that of the former varieties. When the bacterial strains were cultured in vitro, each of them was shown as able to produce the phytohormones auxin, abscisic acid, gibberellins, and cytokinins. The implication is that since the presence in the rhizospere of both Arthrobacter sp. and Bacillus sp. strains can support the growth of maize in salinity-affected and P deficient soils in a genotype-dependent fashion, it is important to not only optimize the PGPR strain used for inoculation, but also to select maize varieties which can benefit most strongly from an association with these bacteria.

Isolation and Characterization of Root-Associated Bacterial Endophytes and Their Biocontrol Potential against Major Fungal Phytopathogens of Rice (Oryza sativa L.)

Rice (Oryza sativa L.) is a major cereal food crop worldwide, and its growth and yield are affected by several fungal phytopathogens, including Magnaporthe oryzae, Fusarium graminearum, F. moniliforme, and Rhizoctonia solani. In the present study, we have isolated and characterized root-associated bacterial endophytes that have antifungal activities against rice fungal phytopathogens. A total of 122 root-associated bacterial endophytes, belonging to six genera (Bacillus, Fictibacillus, Lysinibacillus, Paenibacillus, Cupriavidus, and Microbacterium) and 22 species were isolated from three rice cultivars. Furthermore, the 16S rRNA sequence-based phylogeny results revealed that Bacillus was the most dominant bacterial genera, and that there were 15 different species among the isolates. Moreover, 71 root-associated endophytes showed antagonistic effects against four major fungal phytopathogens, including M. oryzae, F. graminearum,F. moniliforme, and R. solani. Additionally, the biochemical, physiological, and PCR amplification results of the antibiotic-related genes further supported the endophytes as potential biocontrolling agents against the rice fungal pathogens. Consequently, the findings in this study suggested that the isolated bacterial endophytes might have beneficial roles in rice defense responses, including several bioactive compound syntheses. The outcomes of this study advocate the use of natural endophytes as an alternative strategy towards the rice resistance response.

Fungal Endophytes Exert Positive Effects on Colobanthus quitensis Under Water Stress but Neutral Under a Projected Climate Change Scenario in Antarctica

Functional symbiosis is considered one of the successful mechanisms by which plants that inhabit extreme environment improve their ability to tolerate different types of stress. One of the most conspicuous type of symbiosis is the endophyticism. This interaction has been noted to play a role in the adaptation of the native vascular plant Colobanthus quitensis to the stressful environments of Antarctica, characterized by low temperatures and extreme aridity. Projections of climate change for this ecosystem indicate that abiotic conditions will be less limiting due to an increase in temperature and water availability in the soil. Due to this decrease in stress induced by the climate change, it has been suggested that the positive role of fungal endophytes on performance of C. quitensis plants would decrease. In this study, we evaluated the role of endophytic fungi on osmoprotective molecules (sugar production, proline, oxidative stress) and gene expression (CqNCED1, CqABCG25, and CqRD22) as well as physiological traits (stomatal opening, net photosynthesis, and stomatal conductance) in individuals of C. quitensis. Individual plants of C. quitensis with (E+) and without (E-) endophytic fungi were exposed to simulated conditions of increased water availability (W+), having the current limiting water condition (W-) in Antarctica as control. The results reveal an endophyte-mediated lower oxidative stress, higher production of sugars and proline in plants. In addition, E+ plants showed differential expressions in genes related with drought stress response, which was more evident in W- than in W+. These parameters corresponded with increased physiological mechanisms such as higher net photosynthesis, stomatal opening and conductance under presence of endophytes (E+) as well as the projected water condition (W+) for Antarctica. These results suggest that the presence of fungal endophytes plays a positive role in favoring tolerance to drought in C. quitensis. However, this positive role would be diminished if the stress factor is relaxed, suggesting that the role of endophytes could be less important under a future scenario of climate change in Antarctica with higher soil water availability.

Beneficial Effects of Endophytic Fungi from the Anoectochilus and Ludisia Species on the Growth and Secondary Metabolism of Anoectochilus roxburghii

Endophytic fungi possess favorable effects on their host plants, including disease-resistance improvement, secondary metabolite induction, and growth promotion. It is therefore a promising and sustainable strategy to utilize endophytic fungi for the quality improvement of medicinal herbs or important crops. In our study, a collection of 277 strains of endophytic fungi were isolated from Anoectochilus and Ludisia orchids. Two strains J162 and J211 can be symbiotically cocultured with the tissue culture seedlings of Anoectochilus roxburghii, a popular medicinal and edible plant in southern China. Both strains can significantly enhance the biomass of A. roxburghii and induce the biosynthesis and accumulation of its active ingredients, including flavonoids, kinsenoside, and polysaccharides. J162 and J211 were further identified as Chaetomium globosum and Colletotrichum gloeosporioides based on multilocus phylogenetic analysis. Immunocytochemical staining indicated that J162 and J211 mainly colonized the intercellular gap of xylem parenchyma cells of A. roxburghii roots without obvious harm. In addition, quantitative real-time polymerase chain reaction showed that the expression of three growth-related genes, namely, uracil phosphoribosyl transferase, amino acid transmembrane transporter, and maturase K, were significantly altered in A. roxburghii plants when treated with J162 and J211. In conclusion, the two strains are highly beneficial microbial resources for the growth and accumulation of active ingredients of A. roxburghii in agricultural cultivation.

Community Structure, Diversity and Potential of Endophytic Bacteria in the Primitive New Zealand Medicinal Plant Pseudowintera colorata

Although the importance of the plant microbiome in commercial plant health has been well established, there are limited studies in native medicinal plants. Pseudowintera colorata (horopito) is a native New Zealand medicinal plant recognized for its antimicrobial properties. Denaturing gradient gel electrophoresis (DGGE) and Illumina MiSeq analysis of P. colorata plants from ten sites across New Zealand showed that tissue type strongly influenced the diversity and richness of endophytic bacteria (PERMANOVA, P < 0.05). In addition, two OTUs belonging to the genus Pseudomonas (Greengenes ID: 646549 and 138914) were found to be present in >75% of all P. colorata leaf, stem and root samples and were identified as the members of the P. colorata “core endomicrobiome”. Culture-independent analysis was complemented by the recovery of 405 endophytic bacteria from the tissues of P. colorata. Some of these cultured endophytic bacteria (n = 10) showed high antagonism against four different phytopathogenic fungi tested. The influence of endophytic bacteria on plant growth was assessed by inoculating P. colorata seedlings. The mean shoot height of seedlings treated with Bacillus sp. TP1LA1B were longer (1.83×), had higher shoot dry weight (1.8×) and produced more internodes (1.8×) compared to the control.

Agricultural and Other Biotechnological Applications Resulting from Trophic Plant-Endophyte Interactions

Endophytic microbiota plays a role not only in supplying plants with the basic nutrients indispensable for their growth, but also helps them in the mechanisms of adaptation to various environmental stresses (i.e., salinity, drought), which is important in the aspect of crop yields. From the agricultural and biotechnological points of view, the knowledge of endophytes and their roles in increasing crop yields, plant resistance to diseases, and helping to survive environmental stress is extremely desirable. This paper reviews some of the beneficial plant–microbe interactions that might be potentially used in both agriculture (plant growth stimulation effect, adaptation of host organisms in salinity and drought conditions, and support of defense mechanisms in plants), and in biotechnology (bioactive metabolites, application of endophytes for bioremediation and biotransformation processes, and production of biofertilizers and biopreparations). Importantly, relatively recent reports on endophytes from the last 10 years are summarized in this paper.

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.

Research Progress and Perspective on Drought Stress in Legumes: A Review

Climate change, food shortage, water scarcity, and population growth are some of the threatening challenges being faced in today's world. Drought stress (DS) poses a constant challenge for agricultural crops and has been considered a severe constraint for global agricultural productivity; its intensity and severity are predicted to increase in the near future. Legumes demonstrate high sensitivity to DS, especially at vegetative and reproductive stages. They are mostly grown in the dry areas and are moderately drought tolerant, but severe DS leads to remarkable production losses. The most prominent effects of DS are reduced germination, stunted growth, serious damage to the photosynthetic apparatus, decrease in net photosynthesis, and a reduction in nutrient uptake. To curb the catastrophic effect of DS in legumes, it is imperative to understand its effects, mechanisms, and the agronomic and genetic basis of drought for sustainable management. This review highlights the impact of DS on legumes, mechanisms, and proposes appropriate management approaches to alleviate the severity of water stress. In our discussion, we outline the influence of water stress on physiological aspects (such as germination, photosynthesis, water and nutrient uptake), growth parameters and yield. Additionally, mechanisms, various management strategies, for instance, agronomic practices (planting time and geometry, nutrient management), plant growth-promoting Rhizobacteria and arbuscular mycorrhizal fungal inoculation, quantitative trait loci (QTLs), functional genomics and advanced strategies (CRISPR-Cas9) are also critically discussed. We propose that the integration of several approaches such as agronomic and biotechnological strategies as well as advanced genome editing tools is needed to develop drought-tolerant legume cultivars.

Antagonism and antibiotic resistance drive a species-specific plant microbiota differentiation in Echinacea spp

A key factor in the study of plant-microbes interactions is the composition of plant microbiota, but little is known about the factors determining its functional and taxonomic organization. Here we investigated the possible forces driving the assemblage of bacterial endophytic and rhizospheric communities, isolated from two congeneric medicinal plants, Echinacea purpurea (L.) Moench and Echinacea angustifolia (DC) Heller, grown in the same soil, by analysing bacterial strains (isolated from three different compartments, i.e. rhizospheric soil, roots and stem/leaves) for phenotypic features such as antibiotic resistance, extracellular enzymatic activity, siderophore and indole 3-acetic acid production, as well as cross-antagonistic activities. Data obtained highlighted that bacteria from different plant compartments were characterized by specific antibiotic resistance phenotypes and antibiotic production, suggesting that the bacterial communities themselves could be responsible for structuring their own communities by the production of antimicrobial molecules selecting bacterial-adaptive phenotypes for plant tissue colonization.

Potential role of weather, soil and plant microbial communities in rapid decline of apple trees

An unusual decline and collapse of young established trees known as “rapid apple decline” (RAD) has become a major concern for apple growers, particularly in the northeastern United States. This decline is characterized by stunted growth, pale yellow to reddish leaves, and tree collapse within weeks after onset of symptoms. We studied declining apple trees to identify potential involvement of abiotic and biotic stresses. We used 16S and ITS to profile bacterial and fungal communities in the soil, rhizosphere, roots, and shoots and tested for the presence of six viruses in scions and rootstocks of symptomatic and asymptomatic trees. The viruses detected were not associated with RAD symptoms. Bacterial and fungal populations were highly variable in plant tissue, soil and rhizosphere samples, with bacteroidetes, firmicutes, proteobacteria, acidobacteria, and actinobacteria the predominant bacterial classes in various samples. ‘Alphaproteobacteria-rickettsiales’, a bacterial class usually reduced in water-limiting soils, had significantly low abundance in root samples of symptomatic trees. Basidiomycota and Ascomycota fungal classes were the most common fungal classes observed, but neither showed differential enrichment between symptomatic and asymptomatic trees. Analyzing weather data showed an extremely cold winter followed by drought in 2015–2016, which likely weakened the trees to make them more susceptible to varied stresses. In addition, similar physical and nutritional soil composition from symptomatic and asymptomatic trees rules out the role of nutritional stress in RAD. Necrotic lesions and wood decay symptoms dispersing from bark or vascular cambium towards the heartwood were observed primarily below the graft union of declining apple trees, suggesting that the rootstock is the originating point of RAD. We speculate that differences in abiotic factors such as moisture levels in declining roots in combination with extreme weather profiles might cause RAD but cannot clearly rule out the involvement of other factors.

Synergism of Pseudomonas aeruginosa (LSE-2) nodule endophyte with Bradyrhizobium sp. (LSBR-3) for improving plant growth, nutrient acquisition and soil health in soybean

The present study was aimed to assess the scope of native potential endophyte Pseudomonas aeruginosa (LSE-2) strain (KX925973) with recommended Bradyrhizobium sp. (LSBR-3) (KF906140) for synergistic effect to develop as consortium biofertilizer of soybean. A total of 28 non-rhizobial endophytic bacteria were isolated from cultivated and wild sp. of soybean. All isolates were screened for multifarious PGP traits viz. Indole-3-acetic acid (IAA), phosphate (P) and zinc (Zn) solubilization, siderophore, cell wall degrading enzymes and pathogenicity. Compatible of LSBR-3 and LSE-2 enhanced IAA, P-solubilization, 1-aminocyclopropane-carboxylate deaminase and biofilm formation over the single inoculant treatment. Further, consortium was evaluated in vivo for growth, symbiotic traits, nutrient acquisition, soil quality parameters and yield attributes of soybean. Improvement in growth parameters were recorded with dual inoculant LSBR-3 + LSE-2 as compared to LSBR-3 alone and un-inoculated control treatments. Significantly (p ≥ 0.05) high symbiotic and soil quality parameters (phosphatase and soil dehydrogenase activity) was recorded with LSBR-3 + LSE-2 at vegetative and flowering stage as compared to LSBR-3 alone and un-inoculated control treatments. Single inoculation of LSBR-3 improved grain yield by 4.25% over the un-inoculated control treatment, further, enhancement in yield was recorded with consortium inoculant (LSBR-3 and LSE-2) by 3.47% over the LSBR-3 alone. Application of consortium inoculant (LSBR-3 + LSE-2) gave an additional income of Rs. 5089/ha over the un-inoculated control treatment. The results, thus strongly suggest that endophytic diazotroph LSE-2 can be used as potent bio-inoculant along with LSBR-3 as bio-enhancer for improving soybean productivity in a sustainable system.

Diversity and Functionality of Culturable Endophytic Bacterial Communities in Chickpea Plants

The aims of this study were to isolate, identify and characterize culturable endophytic bacteria from chickpea (Cicer arietinum L.) roots grown in different soils. In addition, the effects of rhizobial inoculation, soil and stress on the functionality of those culturable endophytic bacterial communities were also investigated. Phylogenetic analysis based on partial 16S rRNA gene sequences revealed that the endophytic bacteria isolated in this work belong to the phyla Proteobacteria, Firmicutes and Actinobacteria, with Enterobacter and Pseudomonas being the most frequently observed genera. Production of indoleacetic acid and ammonia were the most widespread plant growth-promoting features, while antifungal activity was relatively rare among the isolates. Despite the fact that the majority of bacterial endophytes were salt- and Mn-tolerant, the isolates obtained from soil with Mn toxicity were generally more Mn-tolerant than those obtained from the same soil amended with dolomitic limestone. Several associations between an isolate's genus and specific plant growth-promoting mechanisms were observed. The data suggest that soil strongly impacts the Mn tolerance of endophytic bacterial communities present in chickpea roots while rhizobial inoculation induces significant changes in terms of isolates' plant growth-promoting abilities. In addition, this study also revealed chickpea-associated endophytic bacteria that could be exploited as sources with potential application in agriculture.

Culturable endophytic fungal communities associated with plants in organic and conventional farming systems and their effects on plant growth

As compared to organic farming system, conventional farming system relies on higher inputs of synthetic agrochemicals, which may reduce the abundance, diversity, and beneficial effects of plant endophytic fungal communities. This study compares the diversity and abundance of culturable endophytic fungal communities associated with four plant species –corn, tomato, pepper, and watermelon grown in separate organic and conventional fields. In all, 740 fungal isolates were identified, of which 550 were from the organic fields and 190 from the conventional ones. These fungal isolates were grouped into eight orders and 22 species, with the two most abundant species being Trichoderma sp. and Pichia guilliermondi. The fungal species diversity and abundance were both significantly higher in the organic than in the conventional fields. All the isolated endophytic fungi improved tomato plants’ shoot growth and biomass significantly, as compared with the water control. Six fungal isolates also exhibited activity that enhanced tomato fruit yields. These results suggest that these endophytic fungi might be a considerable boost to sustainable agricultural production, while also reducing the agricultural application of chemicals and thus benefiting the environment and human health.

Metabolic and proteomic alteration in phytohormone-producing endophytic Bacillus amyloliquefaciens RWL-1 during methanol utilization

INTRODUCTION

Methanol utilization by bacteria is important for various industrial processes. Methylotrophic bacteria are taxonomically diverse and some species promote plant growth and induce stress tolerance. However, methylotrophic potential of bacterial endophytes is poorly understood.

OBJECTIVE

The current study aimed to evaluate the metabolomic and proteomic changes in endophytic Bacillus amyloliquefaciens RWL-1 caused by its methanol utilization and the resultant influence on its phytohormone production.

METHODS

B. amyloliquefaciens RWL-1 was grown in LB medium with different concentrations [0 (control), 0.5, 1, 1.5, 2, 2.5, 3, 3.5, and 4%) of methanol to examine its methylotrophic potential. SDS-PAGE analysis was carried out for bacterial protein confirmation. Moreover, the phytohormones (indole 3 acetic acid (IAA), gibberellins (GAs), abscisic acid (ABA)) produced by RWL-1 in methanol supplemented medium were quantified by GC-MS/SIM (6890N Network GC system, and 5973 Network Mass Selective Detector; Agilent Technologies, Santa Clara, CA, USA), while the antioxidants were estimated spectrophotometrically (T60 UV-VIS spectrophotometer, Leicester, UK). The amino acid quantification was carried out by amino acid analyzer (HITACHI L-8900, Japan). Furthermore, Nano-liquid chromatography (LC)-MS/MS analysis was performed with an Agilent system (Wilmington, DE, USA) for proteomic analysis while mascot algorithm (Matrix science, USA) was used to identify peptide sequences present in the protein sequence database.

RESULTS

RWL-1 showed significant growth in media supplemented with 2 and 3.5% methanol, when compared with other concentrations. Mass spectroscopy analysis revealed that RWL-1 utilizes methanol efficiently as a carbon source. In the presence of methanol, RWL-1 produced significantly higher levels of IAA but lower levels of ABA, when compared with the control. Further, enzymatic antioxidants and functional amino acids were significantly up-regulated, with predominant expression of glutamic acid and alanine. Nano-liquid chromatography, quadrupole time-of-flight analysis, and quantitative analysis of methanol-treated bacterial cells showed expression of eight different types of proteins, including detoxification proteins, unrecognized and unclassified enzymes with antioxidant properties, proteases, metabolism enzymes, ribosomal proteins, antioxidant proteins, chaperones, and heat shock proteins.

CONCLUSION

Results demonstrate that RWL-1 can significantly enhance its growth by utilizing methanol, and could produce phytohormones when growing in methanol-supplemented media, with increased expression of specific proteins and different biochemicals. These results will be useful in devising strategies for utilizing methylotrophic bacterial endophytes as alternative promoters of plant growth. Understanding RWL-1 ability to utilize methanol. The survival and phytohormones production by Bacillus amyloliquefaciens RWL-1 in methanol supplemented media whistle inducing metabolic and proteomic changes.

Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range

Increasing evidence has confirmed the importance of plant-associated bacteria for plant growth and productivity, and thus it is hypothesized that interactions between bacteria and alien plants might play an important role in plant invasions. However, the diversity of the bacterial communities associated with invasive plants is poorly understood. We therefore investigated the diversity of rhizospheric and endophytic bacteria associated with the invasive annual plant Senecio vulgaris L. (Asteraceae) based on 16S rRNA gene data obtained from 57 samples of four Senecio vulgaris populations in a subtropical mountainous area in central China. Significant differences in diversity were observed between plant compartments. Specifically, the rhizosphere harbored many more bacterial operational taxonomic units and showed higher alpha diversity than the leaf and root endospheres. The relative abundance profiles of the bacterial community composition differed substantially between the compartments and populations, especially at the phylum and family levels. However, the top five phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Acidobacteria) accounted for more than 90% of all the bacterial communities. Moreover, similar endophytic communities with a shared core set of bacteria were observed from different Senecio vulgaris populations. Heavy-metal-resistant, phosphate-solubilizing bacteria (Brevundimonas diminuta), nitrogen-fixing bacteria (Rhizobium leguminosarum), and cold-resistant bacteria (Exiguobacterium sibiricum) were present in the endosphere at relatively high abundance. This study, which reveals the structure of bacterial communities and their putative function in invasive Senecio vulgaris plants, is the first step in investigating the role of plant-bacteria interactions in the invasion of this species in China.

1-Aminocyclopropane-1-carboxylic acid deaminase producing beneficial rhizobacteria ameliorate the biomass characters of Panicum maximum Jacq. by mitigating drought and salt stress

1-Aminocyclopropane-1-carboxylic acid (ACC) is a precursor molecule of ethylene whose concentration is elevated in the plant subjected to biotic and abiotic stress. Several soil microorganisms are reported to produce ACC deaminase (ACCd) which degrades ACC thereby reducing stress ethylene in host plants. This study is aimed to apply ACCd producing beneficial rhizobacteria to improve biochemical parameters and cell wall properties of Panicum maximum exposed to salt and drought stress, focusing on bioethanol production. Thirty-seven ACCd producing bacteria isolated from rhizospheric soil of field grown P. maximum and 13 were shortlisted based on their beneficial traits (root colonization, production of indole acetic acid, siderophore, hydrogen cyanide, phosphate solubilization, biofilm formation, tolerance to salt and Polyethylene glycol) and a total score obtained. All shortlisted bacteria were found significant in enhancing the plant growth, water conservation, membrane stability, biocompatible solutes and protein, phenolic contents and photosynthetic pigments in plants grown under stress conditions. Cell wall composition (Cellulose, Hemicellulose and Lignin) of the treated plants grown under stress conditions recorded a significant improvement over their respective controls and found equivalent to the plants grown under normal circumstances. Biomass from bacterial treatment recorded higher total reducing sugars upon pre-treatment and hydrolysis, and theoretical bioethanol yield.

Rhizophagy Cycle: An Oxidative Process in Plants for Nutrient Extraction from Symbiotic Microbes

In this paper, we describe a mechanism for the transfer of nutrients from symbiotic microbes (bacteria and fungi) to host plant roots that we term the ‘rhizophagy cycle.’ In the rhizophagy cycle, microbes alternate between a root intracellular endophytic phase and a free-living soil phase. Microbes acquire soil nutrients in the free-living soil phase; nutrients are extracted through exposure to host-produced reactive oxygen in the intracellular endophytic phase. We conducted experiments on several seed-vectored microbes in several host species. We found that initially the symbiotic microbes grow on the rhizoplane in the exudate zone adjacent the root meristem. Microbes enter root tip meristem cells—locating within the periplasmic spaces between cell wall and plasma membrane. In the periplasmic spaces of root cells, microbes convert to wall-less protoplast forms. As root cells mature, microbes continue to be subjected to reactive oxygen (superoxide) produced by NADPH oxidases (NOX) on the root cell plasma membranes. Reactive oxygen degrades some of the intracellular microbes, also likely inducing electrolyte leakage from microbes—effectively extracting nutrients from microbes. Surviving bacteria in root epidermal cells trigger root hair elongation and as hairs elongate bacteria exit at the hair tips, reforming cell walls and cell shapes as microbes emerge into the rhizosphere where they may obtain additional nutrients. Precisely what nutrients are transferred through rhizophagy or how important this process is for nutrient acquisition is still unknown.

Endophytic Bacterial Community Structure and Function of Herbaceous Plants From Petroleum Hydrocarbon Contaminated and Non-contaminated Sites

Bacterial endophytes (BEs) are non-pathogenic residents of healthy plant tissues that can confer benefits to plants. Many Bacterial endophytes have been shown to contribute to plant growth and health, alleviation of plant stress and to in-planta contaminant-degradation. This study examined the endophytic bacterial communities of plants growing abundantly in a heavily hydrocarbon contaminated site, and compared them to those found in the same species at a non-contaminated. We used culture- dependent and independent methods to characterize the community structure, hydrocarbon degrading capabilities, and plant growth promoting traits of cultivable endophytes isolated from Achillea millefolium, Solidago Canadensis, and Daucus carota plants from these two sites. Culture- dependent and independent analyses revealed class Gammaproteobacteria predominated in all the plants regardless of the presence of petroleum hydrocarbon, with Pantoea spp. as largely dominant. It was interesting to note a >50% taxonomic overlap (genus level) of 16s rRNA high throughput amplicon sequences with cultivable endophytes. PERMANOVA analysis of TRFLP fragments revealed significant structural differences between endophytic bacterial communities from hydrocarbon-contaminated and non-contaminated soils-however, there was no marked difference in their functional capabilities. Pantoea spp. demonstrated plant beneficial characteristics, such as P solubilization, indole-3-acetic acid production and presence of 1-aminocyclopropane-1-carboxylate deaminase. Our findings reveal that functional capabilities of bacterial isolates being examined were not influenced by the presence of contamination; and that the stem endosphere supports ubiquitous BEs that were consistent throughout plant hosts and sites.

The culturable endophytic fungal communities of switchgrass grown on a coal-mining site and their effects on plant growth

Plants have a diverse endophytic microbiome that is functionally important for their growth, development, and health. In this study, the diversity and specificity of culturable endophytic fungal communities were explored in one of the most important biofuel crops, switchgrass plants (Panicum virgatum L.), which have been cultivated on a reclaimed coal-mining site for more than 20 years. The endophytic fungi were isolated from the surface-sterilized shoot (leaf and stem), root, and seed tissues of switchgrass plants and then cultured for identification. A total of 1339 fungal isolates were found and 22 operational taxonomic units (OTUs) were sequence identified by internal transcribed spacer (ITS) primers and grouped into 7 orders and 4 classes. Although a diverse range of endophytic fungi associated with switchgrass were documented, the most abundant class, order, and species were Sordariomycetes, Hypocreales, and Fusarium spp. respectively. About 86% of the isolated endophytic fungi were able to enhance the heights of the shoots; 69% could increase the shoot fresh weights; and 62% could improve the shoot dry weights after being reintroduced back into the switchgrass plants, which illustrated their functional importance. Through the Shannon Diversity Index analysis, we observed a gradation of species diversity, with shoots and roots having the similar values and seeds having a lesser value. It was observed that the switchgrass plants showing better growth performance displayed higher endophytic fungal species diversity and abundance. It was also discovered that the rhizosphere soil organic matter content was positively correlated with the fungal species diversity. All these data demonstrate the functional association of these beneficial endophytic fungi with switchgrass and their great potential in improving the switchgrass growth and biomass to benefit the biofuel industry by reducing chemical inputs and burden to the environment.

Molecular Insights into the Involvement of a Never Ripe Receptor in the Interaction Between Two Beneficial Soil Bacteria and Tomato Plants Under Well-Watered and Drought Conditions

Management of plant growth-promoting bacteria (PGPB) can be implemented to deal with sustainable intensification of agriculture. Ethylene is an essential component for plant growth and development and in response to drought. However, little is known about the effects of bacterial inoculation on ethylene transduction pathway. Thus, the present study sought to establish whether ethylene perception is critical for growth induction by two different PGPB strains under drought conditions and the analysis of bacterial effects on ethylene production and gene expression in tomatoes (Solanum lycopersicum). The ethylene-insensitive never ripe (nr) and its isogenic wild-type (wt) cv. Pearson line were inoculated with either Bacillus megaterium or Enterobacter sp. strain C7 and grown until the attainment of maturity under both well-watered and drought conditions. Ethylene perception is crucial for B. megaterium. However, it is not of prime importance for Enterobacter sp. strain C7 PGPB activity under drought conditions. Both PGPB decreased the expression of ethylene-related genes in wt plants, resulting in stress alleviation, while only B. megaterium induced their expression in nr plants. Furthermore, PGPB inoculation affected transcriptomic profile dependency on strain, genotype, and drought. Ethylene sensitivity determines plant interaction with PGPB strains. Enterobacter sp. strain C7 could modulate amino-acid metabolism, while nr mutation causes a partially functional interaction with B. megaterium, resulting in higher oxidative stress and loss of PGPB activity.

High-Throughput Sequencing Analysis of Endophytic Bacteria Diversity in Fruits of White and Red Pitayas from Three Different Origins

Pitaya contains various types of polyphenols, flavonoid and vitamins which are beneficial for health and it is among the most important commercial tropical fruits worldwide. Endophytic bacteria might be beneficial for plant growth and yield. However, bacterial diversity in pitaya is poorly characterized. In this study, fruits of white and red pitayas from three different origins (Thailand, Vietnam and China) were chosen for endophytic bacteria diversity investigation by using Illumina HiSeq second-generation high-throughput sequencing technology. Large number of endophytic bacteria were detected and 22 phyla, 56 classes, 81 orders, 122 families and 159 genera were identified. Endophytic bacteria diversity was uneven among pitaya fruits from different origins and bacteria structure was different between white pitaya group and red pitaya group. Phylum Bacteroidetes, classes Bacteroidia and Coriobacteriia, orders Bacteroidales and Coriobacteriales, families Prevotellaceae, Bacteroidaceae, Ruminococcaceae, Paraprevotellaceae, Rikenellaceae, Alcaligenaceae and Coriobacteriaceae, genera Prevotella, Bacteroides, Roseburia, Faecalibacterium and Sutterella were statistically significant different species (P < 0.05) between white and red pitayas. These findings might be useful for growth improvement, fruit preservation and processing of different pitaya species from different origins.

Dyella-Like Bacterium Isolated from an Insect as a Potential Biocontrol Agent Against Grapevine Yellows

Yellows diseases, caused by phytopathogenic bacteria of the genus Phytoplasma, are a major threat to grapevines worldwide. Because conventional applications against this pathogen are inefficient and disease management is highly challenging, the use of beneficial bacteria has been suggested as a biocontrol solution. A Dyella-like bacterium (DLB), isolated from the Israeli insect vector of grapevine yellows (Hyalesthes obsoletus), was suggested to be an endophyte. To test this hypothesis, the bacterium was introduced by spraying the plant leaves, and it had no apparent phytotoxicity to grapevine. Fluorescent in situ hybridization analysis showed that DLB is colonizing grapevine phloem. Because phytoplasmas inhabit the same niche, DLB interactions with this phytopathogen were examined. When the isolate was introduced to phytoplasma-infected Chardonnay plantlets, morphological disease symptoms were markedly reduced. The mode of DLB action was then tested using bioinformatics and system biology tools. DLB genome analysis suggested that the ability to reduce phytoplasma symptoms is related to inhibition of the pathogenic bacterium. These results provide the first step in examining the potential of DLB as a biological control agent against phytoplasmas in grapevine and, possibly, other agricultural crops.

Bacterial Endophytes in Plant Tissue Culture: Mode of Action, Detection, and Control

Endophytic bacteria have been increasingly in the focus of research projects during the last decade. This has changed the view on bacteria in plant tissue culture and led to the differentiation between artificially introduced contaminations and naturally occurring endophytes with neutral, negative, or positive impact on the plant propagation process. This review chapter gives an overview on recent findings about the impact that bacteria have on the plant physiology in general and during micropropagation. Additionally, methods for the detection and identification of bacteria in plant tissue are described and, finally, suggestions of how to deal with bacterial endophytes in in vitro culture are given.