Application of bacteria from non-cultivated plants to promote growth, alter root architecture and alleviate salt stress of cotton

Endophyte mediated biocontrol mechanisms of phytopathogens in agriculture

The global human population is growing and demand for food is increasing. Global agriculture faces numerous challenges, including excessive application of synthetic pesticides, emergence of herbicide-and pesticide-resistant pathogenic microbes, and more frequent natural disasters associated with global warming. Searches for valuable endophytes have increased, with the aim of making agriculture more sustainable and environmentally friendly. Endophytic microbes are known to have a variety of beneficial effects on plants. They can effectively transfer nutrients from the soil into plants, promote plant growth and development, increase disease resistance, increase stress tolerance, prevent herbivore feeding, reduce the virulence of pathogens, and inhibit the growth of rival plant species. Endophytic microbes can considerably minimize the need for agrochemicals, such as fertilizers, fungicides, bactericides, insecticides, and herbicides in the cultivation of crop plants. This review summarizes current knowledge on the roles of endophytes focusing on their mechanisms of disease control against phytopathogens through the secretion of antimicrobial substances and volatile organic compounds, and the induction of systemic resistance in plants. Additionally, the beneficial roles of these endophytes and their metabolites in the control of postharvest diseases in plants have been summarized.

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.

Comparative analysis of the microbiomes of strawberry wild species Fragaria nilgerrensis and cultivated variety Akihime using amplicon-based next-generation sequencing

Fragaria nilgerrensis is a wild strawberry species widely distributed in southwest China and has strong ecological adaptability. Akihime (F. × ananassa Duch. cv. Akihime) is one of the main cultivated strawberry varieties in China and is prone to infection with a variety of diseases. In this study, high-throughput sequencing was used to analyze and compare the soil and root microbiomes of F. nilgerrensis and Akihime. Results indicate that the wild species F. nilgerrensis showed higher microbial diversity in nonrhizosphere soil and rhizosphere soil and possessed a more complex microbial network structure compared with the cultivated variety Akihime. Genera such as Bradyrhizobium and Anaeromyxobacter, which are associated with nitrogen fixation and ammonification, and Conexibacter, which is associated with ecological toxicity resistance, exhibited higher relative abundances in the rhizosphere and nonrhizosphere soil samples of F. nilgerrensis compared with those of Akihime. Meanwhile, the ammonia-oxidizing archaea Candidatus Nitrososphaera and Candidatus Nitrocosmicus showed the opposite tendencies. We also found that the relative abundances of potential pathogenic genera and biocontrol bacteria in the Akihime samples were higher than those in the F. nilgerrensis samples. The relative abundances of Blastococcus, Nocardioides, Solirubrobacter, and Gemmatimonas, which are related to pesticide degradation, and genus Variovorax, which is associated with root growth regulation, were also significantly higher in the Akihime samples than in the F. nilgerrensis samples. Moreover, the root endophytic microbiomes of both strawberry species, especially the wild F. nilgerrensis, were mainly composed of potential biocontrol and beneficial bacteria, making them important sources for the isolation of these bacteria. This study is the first to compare the differences in nonrhizosphere and rhizosphere soils and root endogenous microorganisms between wild and cultivated strawberries. The findings have great value for the research of microbiomes, disease control, and germplasm innovation of strawberry.

The Contribution of Hormonal Changes to the Protective Effect of Endophytic Bacterium Bacillus subtilis on Two Wheat Genotypes with Contrasting Drought Sensitivities under Osmotic Stress

A comparative analysis was conducted to evaluate the effects of seed priming with endophytic bacterium Bacillus subtilis 10-4 (BS) on the hormonal system and cell wall tolerance (lipid peroxidation (LPO), electrolyte leakage (EL), and root lignin deposition) of two Triticum aestivum L. (wheat) varieties with contrasting drought sensitivities (Ekada 70-drought-tolerant (DT); Salavat Yulaev-drought-sensitive (DS)) under normal conditions and 12% polyethylene glycol-6000 (PEG)-induced osmotic stress. The results showed that under normal conditions, the growth stimulation in wheat plants by BS was attributed to changes in the hormonal balance, particularly an increase in endogenous indole-3-acetic acid (IAA) accumulation. However, under stress, a significant hormonal imbalance was observed in wheat seedlings, characterized by a pronounced accumulation of abscisic acid (ABA) and a decrease in the levels of IAA and cytokinins (CK). These effects were reflected in the inhibition of plant growth. BS exhibited a protective effect on stressed plants, as evidenced by a significantly lower amplitude of stress-induced changes in the hormonal system: maintaining the content of IAA at a level close to the control, reducing stress-induced ABA accumulation, and preventing CK depletion. These effects were further reflected in the normalization of growth parameters in dehydrated seedlings, as well as a decrease in leaf chlorophyll degradation, LPO, and EL, along with an increase in lignin deposition in the basal part of the roots in both genotypes. Overall, the findings demonstrate that BS, producing phytohormones, specifically IAA and ABA, had a more pronounced protective effect on DT plants, as evidenced by a smaller amplitude of stress-induced hormonal changes, higher leaf chlorophyll content, root lignin deposition, and lower cell membrane damage (LPO) and permeability (EL) compared to DS plants.

Harnessing Rhizospheric Microbes for Eco-friendly and Sustainable Crop Production in Saline Environments

Soil salinization is a global issue that negatively impacts crop yield and has become a prime concern for researchers worldwide. Many important crop plants are susceptible to salinity-induced stresses, including ionic and osmotic stress. Approximately, 20% of the world's cultivated and 33% of irrigated land is affected by salt. While various agricultural practices have been successful in alleviating salinity stress, they can be costly and not environment-friendly. Therefore, there is a need for cost-effective and eco-friendly practices to improve soil health. One promising approach involves utilizing microbes found in the vicinity of plant roots to mitigate the effects of salinity stress and enhance plant growth as well as crop yield. By exploiting the salinity tolerance of plants and their associated rhizospheric microorganisms, which have plant growth-promoting properties, it is possible to reduce the adverse effects of salt stress on crop plants. The soil salinization is a common problem in the world, due to which we are unable to use the saline land. To make proper use of this land for different crops, microorganisms can play an important role. Looking at the increasing population of the world, this will be an appreciated effort to make the best use of the wasted land for food security. The updated information on this issue is needed. In this context, this article provides a concise review of the latest research on the use of salt-tolerant rhizospheric microorganisms to mitigate salinity stress in crop plants.

Counteracting action of Bacillus stratosphericus and Staphylococcus succinus strains against deleterious salt effects on Zea mays L

The salinization of soil is the process of progressive accumulation of salts such as sulfates, sodium, or chlorides into the soil. The increased level of salt has significant effects on glycophyte plants, such as rice, maize, and wheat, which are staple foods for the world's population. Consequently, it is important to develop biotechnologies that improve crops and clean up the soil. Among other remediation methods, there is an environmentally friendly approach to ameliorate the cultivation of glycophyte plants in saline soil, namely, the use of microorganisms tolerant to salt with growth-promoting features. Plant growth-promoting rhizobacteria (PGPR) can improve plant growth by colonizing their roots and playing a vital role in helping plants to establish and grow in nutrient-deficient conditions. Our research aimed to test in vivo halotolerant PGPR, isolated and characterized in vitro in a previous study conducted in our laboratory, inoculating them on maize seedlings to improve their growth in the presence of sodium chloride. The bacterial inoculation was performed using the seed-coating method, and the produced effects were evaluated by morphometric analysis, quantization of ion contents (sodium, potassium), produced biomass, both for epigeal (shoot) and hypogeal (root) organs, and by measuring salt-induced oxidative damage. The results showed an increase in biomass and sodium tolerance and even a reduction of oxidative stress in seedlings pretreated with a PGPR bacterial consortium (Staphylococcus succinus + Bacillus stratosphericus) over the control. Moreover, we observed that salt reduces growth and alters root system traits of maize seedlings, while bacterial treatment improves plant growth and partially restores the root architecture system in saline stress conditions. Therefore, the PGPR seed-coating or seedling treatment could be an effective strategy to enhance sustainable agriculture in saline soils due to the protection of the plants from their inhibitory effect.

Salinity Alleviation and Reduction in Oxidative Stress by Endophytic and Rhizospheric Microbes in Two Rice Cultivars

Increased soil salinity poses serious limitations in crop yield and quality; thus, an attempt was made to explore microbial agents to mitigate the ill effects of salinity in rice. The hypothesis was mapping of microbial induction of stress tolerance in rice. Since the rhizosphere and endosphere are two different functional niches directly affected by salinity, it could be very crucial to evaluate them for salinity alleviation. In this experiment, endophytic and rhizospheric microbes were tested for differences in salinity stress alleviation traits in two rice cultivars, CO51 and PB1. Two endophytic bacteria, Bacillus haynesii 2P2 and Bacillus safensis BTL5, were tested with two rhizospheric bacteria, Brevibacterium frigoritolerans W19 and Pseudomonas fluorescens 1001, under elevated salinity (200 mM NaCl) along with Trichoderma viride as an inoculated check. The pot study indicated towards the presence of variable salinity mitigation mechanisms among these strains. Improvement in the photosynthetic machinery was also recorded. These inoculants were evaluated for the induction of antioxidant enzymes viz. CAT, SOD, PO, PPO, APX, and PAL activity along with the effect on proline levels. Modulation of the expression of salt stress responsive genes OsPIP1, MnSOD1, cAPXa, CATa, SERF, and DHN was assessed. Root architecture parameters viz. cumulative length of total root, projection area, average diameter, surface area, root volume, fractal dimension, number of tips, and forks were studied. Confocal scanning laser microscopy indicated accumulation of Na⁺ in leaves using cell impermeant Sodium Green™, Tetra (Tetramethylammonium) Salt. It was found that each of these parameters were induced differentially by endophytic bacteria, rhizospheric bacteria, and fungus, indicating different paths to complement one ultimate plant function. The biomass accumulation and number of effective tillers were highest in T4 (Bacillus haynesii 2P2) plants in both cultivars and showed the possibility of cultivar specific consortium. These strains and their mechanisms could form the basis for further evaluating microbial strains for climate-resilient agriculture.

Plant Beneficial Bacteria and Their Potential Applications in Vertical Farming Systems

In this literature review, we discuss the various functions of beneficial plant bacteria in improving plant nutrition, the defense against biotic and abiotic stress, and hormonal regulation. We also review the recent research on rhizophagy, a nutrient scavenging mechanism in which bacteria enter and exit root cells on a cyclical basis. These concepts are covered in the contexts of soil agriculture and controlled environment agriculture, and they are also used in vertical farming systems. Vertical farming-its advantages and disadvantages over soil agriculture, and the various climatic factors in controlled environment agriculture-is also discussed in relation to plant-bacterial relationships. The different factors under grower control, such as choice of substrate, oxygenation rates, temperature, light, and CO₂ supplementation, may influence plant-bacterial interactions in unintended ways. Understanding the specific effects of these environmental factors may inform the best cultural practices and further elucidate the mechanisms by which beneficial bacteria promote plant growth.

Dynamic changes in the endophytic bacterial community during maturation of Amorphophallus muelleri seeds

The seed microbiota is considered to be the starting point of the accumulation of plant microbiota, which is conducive to the preservation and germination of seeds and the establishment and development of seedlings. Our understanding of the colonization and migration dynamics of microbial taxa during seed development and maturation is still limited. This study used 16S rRNA high-throughput sequencing to investigate the dynamic changes in the composition and diversity of the endophytic bacterial community during maturation of Amorphophallus muelleri seeds. The results showed that as seeds matured (green to red), the Shannon index of their endophytic bacterial community first decreased and then increased, and the ACE and Chao1 indices of the endophytic bacterial community decreased gradually. The Shannon, ACE, and Chao1 indices of the endophytic bacterial community in the seed coat first decreased and then increased. Principal coordinate analysis of the bacterial communities revealed that the seed coat at different maturity stages showed significantly distinct bacterial communities and formed different clusters according to maturity stage. The bacterial communities of green and red seeds showed a clear separation, but they both overlapped with those of yellow seeds, indicating that some core taxa were present throughout seed maturation, but their relative abundance was dynamically changing. As the seeds grew more mature, the relative abundance of some bacterial communities with plant growth-promoting traits and others correlated with plant resistance (e.g., Burkholderia-Caballeronia-Paraburkholderia, Bacillus, Pseudomonas, Bradyrhizobium, Streptomyces) tended to increase and peaked in fully mature seeds and seed coats. The endophytic bacterial community of A. muelleri seeds seems to be driven by the seed maturation state, which can provide a theoretical basis for a comprehensive understanding of the assembly process of the microbial community during A. muelleri seed maturation.

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

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

Architectural analysis of root system and phytohormone biosynthetic genes expression in wheat (Triticum aestivum L.) inoculated with Penicillium oxalicum

In this study, a fungal plant growth promoter Penicillium oxalicum T4 isolated from non-rhizosphere soil of Arunachal Pradesh, India, was screened for different plant growth promoting traits in a gnotobiotic study. Though inoculation improved the overall growth of the plants, critical differences were observed in root architecture. Confocal Laser Scanning Microscope, Scanning electron microscope and stereo microscopic study showed that inoculated wheat plants could develop profuse root hairs as compared to control. Root scanning indicated improvement in cumulative root length, root area, root volume, number of forks, links, crossings, and other parameters. Confocal scanning laser microscope indicated signs of endophytic colonization in wheat roots. Gene expression studies revealed that inoculation of T4 modulated the genes affecting root hair development. Significant differences were marked in the expression levels of TaRSL4, TaEXPB1, TaEXPB23, PIN-FORMED protein, kaurene oxidase, lipoxygenase, ACC synthase, ACC oxidase, 9-cis-epoxycarotenoid dioxygenase, and ABA 8'-hydroxylase genes. These genes contribute to early plant development and ultimately to biomass accumulation and yield. The results suggested that P. oxalicum T4 has potential for growth promotion in wheat and perhaps also in other cereals.

Microbial amelioration of salinity stress in endangered accessions of Iranian licorice (Glycyrrhiza glabra L.)

BACKGROUND

Glycyrrhiza glabra L. is a medicinal and industrial plant that has gone extinct due to different abiotic stress caused by climate change. To understand how the plant-associated microorganism can support this plant under salinity, we collected sixteen Iranian accessions of G. glabra L., inoculated their rhizomes with Azotobacter sp. (two levels, bacterial treatments, and no-bacterial treatments, and grown them under salinity stress (NaCl levels; 0, and 200 mM).

RESULTS

Two accessions of Bardsir and Bajgah significantly showed higher resistant to salinity, for example by increasing crown diameter (11.05 and 11 cm, respectively) compared to an average diameter of 9.5 in other accessions. Azotobacter inoculation caused a significant increase in plant height and crown diameter. Among studied accessions, Kashmar (46.21%) and Ilam (44.95%) had the highest rate of membrane stability index (MSI). Evaluation of enzyme activity represented that bacterial application under salinity, increased polyphenol oxidase (PPO) (0.21 U mg^-1 protein), peroxidase (POD) (3.09 U mg^-1 protein U mg^-1 protein), and phenylalanine ammonia-lyase (PAL) (17.85 U mg^-1 protein) activity. Darab accession showed the highest increase (6.45%) in antioxidant potential compared with all studied accessions under Azotobacter inoculation. According to principal component analysis (PCA), it was found that the accession of Meshkinshahr showed a more remarkable ability to activate its enzymatic defense system under salt stress. Also, three accessions of Meshkinshahr, Eghlid, and Ilam were categorized in separated clusters than other accessions regarding various studied treatments.

CONCLUSION

Analysis indicated that five accessions of Meshkinshahr, Rabt, Piranshahr, Bardsir, and Kermanshah from the perspective of induced systematic resistance are the accessions that showed a greater morphophysiological and biochemical outcome under salinity. This study suggested that, inoculation of with Azotobacter on selected accession can relieve salt stress and support industrial mass production under abiotic condition.

Histochemical Evidence for Nitrogen-Transfer Endosymbiosis in Non-Photosynthetic Cells of Leaves and Inflorescence Bracts of Angiosperms

Simple Summary

We used light and confocal microscopy to visualize bacteria in leaf and bract cells of more than 30 species in 18 families of seed plants. We detected chemical exchanges between intracellular bacteria and plant cells. We found that endophytic bacteria that show evidence of the transfer of nitrogen to plants are present in non-photosynthetic cells of leaves and bracts of diverse plant species. Nitrogen transfer from bacteria was observed in epidermal cells, various filamentous and glandular trichomes, and other non-photosynthetic cells. The most efficient of the nitrogen-transfer endosymbioses were seen to involve glandular trichomes, as seen in hops (Humulus lupulus) and hemp (Cannabis sativa). Trichome chemistry is hypothesized to function to scavenge oxygen around bacteria to facilitate nitrogen fixation.

Abstract

We used light and confocal microscopy to visualize bacteria in leaf and bract cells of more than 30 species in 18 families of seed plants. Through histochemical analysis, we detected hormones (including ethylene and nitric oxide), superoxide, and nitrogenous chemicals (including nitric oxide and nitrate) around bacteria within plant cells. Bacteria were observed in epidermal cells, various filamentous and glandular trichomes, and other non-photosynthetic cells. Most notably, bacteria showing nitrate formation based on histochemical staining were present in glandular trichomes of some dicots (e.g., Humulus lupulus and Cannabis sativa). Glandular trichome chemistry is hypothesized to function to scavenge oxygen around bacteria and reduce oxidative damage to intracellular bacterial cells. Experiments to assess the differential absorption of isotopic nitrogen into plants suggest the assimilation of nitrogen into actively growing tissues of plants, where bacteria are most active and carbohydrates are more available. The leaf and bract cell endosymbiosis types outlined in this paper have not been previously reported and may be important in facilitating plant growth, development, oxidative stress resistance, and nutrient absorption into plants. It is unknown whether leaf and bract cell endosymbioses are significant in increasing the nitrogen content of plants. From the experiments that we conducted, it is impossible to know whether plant trichomes evolved specifically as organs for nitrogen fixation or if, instead, trichomes are structures in which bacteria easily colonize and where some casual nitrogen transfer may occur between bacteria and plant cells. It is likely that the endosymbioses seen in leaves and bracts are less efficient than those of root nodules of legumes in similar plants. However, the presence of endosymbioses that yield nitrate in plants could confer a reduced need for soil nitrogen and constitute increased nitrogen-use efficiency, even if the actual amount of nitrogen transferred to plant cells is small. More research is needed to evaluate the importance of nitrogen transfer within leaf and bract cells of plants.

Halotolerant Rhizobacteria for Salinity-Stress Mitigation: Diversity, Mechanisms and Molecular Approaches

Agriculture is the best foundation for human livelihoods, and, in this respect, crop production has been forced to adopt sustainable farming practices. However, soil salinity severely affects crop growth, the degradation of soil quality, and fertility in many countries of the world. This results in the loss of profitability, the growth of agricultural yields, and the step-by-step decline of the soil nutrient content. Thus, researchers have focused on searching for halotolerant and plant growth-promoting bacteria (PGPB) to increase soil fertility and productivity. The beneficial bacteria are frequently connected with the plant rhizosphere and can alleviate plant growth under salinity stress through direct or indirect mechanisms. In this context, PGPB have attained a unique position. The responses include an increased rate of photosynthesis, high production of antioxidants, osmolyte accumulation, decreased Na+ ions, maintenance of the water balance, a high germination rate, and well-developed root and shoot elongation under salt-stress conditions. Therefore, the use of PGPB as bioformulations under salinity stress has been an emerging research avenue for the last few years, and applications of biopesticides and biofertilizers are being considered as alternative tools for sustainable agriculture, as they are ecofriendly and minimize all kinds of stresses. Halotolerant PGPB possess greater potential for use in salinity-affected soil as sustainable bioinoculants and for the bioremediation of salt-affected soil.

Seed Endophytic Bacteria of Pearl Millet (Pennisetum glaucum L.) Promote Seedling Development and Defend Against a Fungal Phytopathogen

Seed endophytic bacteria (SEB) are primary symbionts that play crucial roles in plant growth and development. The present study reports the isolation of seven culturable SEB including Kosakonia cowanii (KAS1), Bacillus subtilis (KAS2), Bacillus tequilensis (KAS3), Pantoea stewartii (KAS4), Paenibacillus dendritiformis (KAS5), Pseudomonas aeruginosa (KAS6), and Bacillus velezensis (KAS7) in pearl millet seeds. All the isolates were characterized for their plant growth promoting activities. Most of the SEB also inhibited the growth of tested fungal phytopathogens in dual plate culture. Removal of these SEB from seeds compromised the growth and development of seedlings, however, re-inoculation with the SEB (Kosakonia cowanii, Pantoea stewartii, and Pseudomonas aeruginosa) restored the growth and development of seedlings significantly. Fluorescence microscopy showed inter and intracellular colonization of SEB in root parenchyma and root hair cells. Lipopeptides were extracted from all three Bacillus spp. which showed strong antifungal activity against tested fungal pathogens. Antifungal lipopeptide genes were also screened in Bacillus spp. After lipopeptide treatment, live-dead staining with fluorescence microscopy along with bright-field and scanning electron microscopy (SEM) revealed structural deformation and cell death in Fusarium mycelia and spores. Furthermore, the development of pores in the membrane and leakages of protoplasmic substances from cells and ultimately death of hyphae and spores were also confirmed. In microcosm assays, treatment of seeds with Bacillus subtilis or application of its lipopeptide alone significantly protected seedlings from Fusarium sp. infection.

Seed inhabiting bacterial endophytes of maize promote seedling establishment and provide protection against fungal disease

Bacteria from different crops and plant varieties have been shown to possess enormous growth promotional attributes. The study aimed to investigate the role of the endophytic microbiome of seeds of corn in improving the growth of seedlings of two different varieties of maize crops (K-25 and baby corn). Furthermore, the study also assessed the role of these bacteria in the protection of seedlings from fungal pathogens. Total twenty-three endophytic bacterial strains were isolated from maize seeds and identified using 16S rDNA sequencing. Most of the isolates had the ability to synthesize auxin (70 %) and solubilize phosphate (74 %), while all the isolates showed nitrogen fixation ability. Some isolates also showed antagonistic activity against phytopathogenic fungi including Rhizoctonia solani and Fusarium sp. suggesting their biocontrol potential. The presence of different lipopeptide genes including bacillomycin D, fengycin, iturin A and surfactin was confirmed in some of the isolates. We observed that treating seeds with an antibiotic compromised the seedlings' growth; however, re-inoculation with endophytic isolates (ZM1/Lysinibacillus sp. and ZM2/Paenibacillus dendritiformis) restored the growth of the seedlings in terms of improved root and shoot development in comparison to non-inoculated controls. The colonization of inoculated bacteria on the root surface was visualized using fluorescent microscopy. Seedling protection assay showed that treated seeds (with ZMW8/ Bacillus velezensis) were protected from fungal infestation (Fusarium verticillioides) even after 12 days of inoculation in comparison to the uninoculated control. The study concludes that indigenous seed-associated bacteria of maize play a major role during seed germination, seedling formation and protect them from phytopathogens.

Inter-Genera Colonization of Ocimum tenuiflorum Endophytes in Tomato and Their Complementary Effects on Na+/K+ Balance, Oxidative Stress Regulation, and Root Architecture Under Elevated Soil Salinity

Endophytic bacilli of ethano-botanical plant Ocimum tenuiflorum were screened for salt stress-alleviating traits in tomato. Four promising O. tenuiflorum endophytes (Bacillus safensis BTL5, Bacillus haynesii GTR8, Bacillus paralicheniformis GTR11, and Bacillus altitudinis GTS16) were used in this study. Confocal scanning laser microscopic studies revealed the inter-genera colonization of O. tenuiflorum endophytes in tomato plants, giving insights for widening the applicability of potential endophytes to other crops. Furthermore, in a pot trial under 150 mM NaCl concentration, the inoculated endophytes contributed in reducing salt toxicity and improving recovery from salt-induced oxidative stress by different mechanisms. Reduction in reactive oxygen species (ROS) (sub-cellular H₂O₂ and superoxide) accumulation was observed besides lowering programmed cell death and increasing chlorophyll content. Endophyte inoculation supplemented the plant antioxidant enzyme system via the modulation of enzymatic antioxidants, viz., peroxidase, ascorbate peroxidase, superoxide dismutase, and catalase, apart from increasing proline and total phenolics. Antioxidants like proline have dual roles of antioxidants and osmoregulation, which might also have contributed to improved water relation under elevated salinity. Root architecture, viz., root length, projection area, surface area, average diameter, tips, forks, crossings, and the number of links, was improved upon inoculation, indicating healthy root growth and enhanced nutrient flow and water homeostasis. Regulation of Na⁺/K⁺ balance and water homeostasis in the plants were also evident from the modulation in the expression of abiotic stress-responsive genes, viz., LKT1, NHX1, SOS1, LePIP2, SlERF16, and SlWRKY39. Shoot tissues staining with light-excitable Na⁺ indicator Sodium Green^TM Tetra (tetramethylammonium) salt showed low sodium transport and accumulation in endophyte-inoculated plants. All four endophytes exhibited different mechanisms for stress alleviation and indicated complementary effects on plant growth. Furthermore, this could be harnessed in the form of a consortium for salt stress alleviation. The present study established inter-genera colonization of O. tenuiflorum endophytes in tomato and revealed its potential in maintaining Na⁺/K⁺ balance, reducing ROS, and improving root architecture under elevated salinity.

Cell wall formation pathways are differentially regulated in sugarcane contrasting genotypes associated with endophytic diazotrophic bacteria

Differences in cell wall components between two BNF-contrasting sugarcane genotypes might result from genetic variations particular to the genotype and from the efficiency in diazotrophic bacteria association. Sugarcane is a plant of the grass family (Poaceae) that is highly cultivated in Brazil, as an important energy resource. Commercial sugarcane genotypes may be successfully associated with beneficial endophytic nitrogen-fixing bacteria, which can influence several plant metabolic pathways, such as cell division and growth, synthesis of hormones, and defense compounds. In this study, we investigated how diazotrophic bacteria associated with sugarcane plants could be involved in the regulation of cell wall formation pathways. A molecular and structural characterization of the cell wall was compared between two genotypes of sugarcane with contrasting rates of Biological Nitrogen Fixation (BNF): SP70-1143 (high BNF) and Chunee (low BNF). Differentially expressed transcripts were identified in transcriptomes generated from SP70-1143 and Chunee. Expression profiles of cellulose and lignin genes, which were more expressed in SP70-1134, and callose genes, which were more expressed in Chunee, were validated by RT-qPCR and microscopic analysis of cell wall components in tissue sections. A similar expression profile in both BNF-contrasting genotypes was observed in naturally colonized plants and in plants inoculated with G. diazotrophicus. Cell walls of the high BNF genotype have a greater cellulose content, which might contribute to increase biomass. In parallel, callose was concentrated in the vascular tissues of the low BNF genotype and could possibly represent a barrier for an efficient bacterial colonization and dissemination in sugarcane tissues. Our data show a correlation between the gene profiles identified in the BNF-contrasting genotypes and a successful association with endophytic diazotrophic bacteria.

A Seed-Endophytic Bacillus safensis Strain With Antimicrobial Activity Has Genes for Novel Bacteriocin-Like Antimicrobial Peptides

Bacteriocins are a highly diverse group of antimicrobial peptides that have been identified in a wide range of commensal and probiotic organisms, especially those resident in host microbiomes. Rising antibiotic resistance have fueled renewed research into new drug scaffolds such as antimicrobial peptides for use in therapeutics. In this investigation, we examined mung bean seeds for endophytes possessing activity against human and plant pathogens. We isolated a novel strain of Bacillus safensis, from the contents of surface-sterilized mung bean seed, which we termed B. safensis C3. Genome sequencing of C3 identified three distinct biosynthetic systems that produce bacteriocin-based peptides. C3 exhibited antibacterial activity against Escherichia coli, Xanthomonas axonopodis, and Pseudomonas syringae. Robust antimicrobial activity of B. safensis C3 was observed when C3 was co-cultured with Bacillus subtilis. Using the cell-free supernatant of C3 and cation exchange chromatography, we enriched a product that retained antimicrobial activity against B. subtilis. The peptide was found to be approximately 3.3 kDa in size by mass spectrometry, and resistant to proteolysis by Carboxypeptidase Y and Endoproteinase GluC, suggesting that it is a modified variant of an AS-48 like bacteriocin. Our findings open new avenues into further development of novel bacteriocin-based scaffolds for therapeutic development, as well as further investigations into how our discoveries of bacteriocin-producing plant commensal microorganisms may have the potential for an immediate impact on the safety of food supplies.

Re-vitalizing of endophytic microbes for soil health management and plant protection

Soil health management and increase crop productivity are challenging issues for researchers and scientists. Many research publications have given multiple technological solutions for improving soil health and crop productivity but main problem is sustainability of those technologies under field condition and different agro-climatic zone. Due to the random industrialization, deforestation, mining and other environmental factor reduce soil fertility and human health. Many alternative options e.g., crop rotation, green manuring, integrated farming, biofertilizer (plant-growth-promoting microorganism, microbial consortium of rhizosphere soils), and vermicomposting are available for adapting and improving the soil heath and crop productivity by farmers. Recent trends of new research dimension for sustainable agriculture, endophytic microbes and its consortium is one of the better alternative for increasing crop productivity, soil health and fertility management. However, current trends are focuses on the endophytic microbes, which are present mostly in all plant species. Endophytic microbes are isolated from plant parts-root, shoot, leaf, flower and seeds which have very potential ability of plant growth promotion and bio-controlling agent for enhancing plant growth and development. Mostly plant endophytes showed multi-dimensional (synergistic, mutualistic, symbiotic etc.) interactions within the host plants. It promotes the plant growth, protects from pathogen, and induces resistance against biotic and abiotic environmental stresses, and improves the soil fertility. Till date, most of the scientific research has been done on assuming that interaction of plant endophytes with the host is similar like the plant-growth-promoting microorganism (PGPM). It would be very interesting to explore the functional properties of plant endophytes to modulate the essential gene expression during biotic and abiotic stresses. Endophytes have the ability to induce the soil fertility by improving soil essential nutrient, enzymatic activity and influence the other physiochemical property. In this study, we have discussed details about functional properties of plant endophytes and their mechanism for enhancing plant productivity and soil health and fertility management under climate-resilient agricultural practices. Our main objective is to promote and explore the beneficial plant endophytes for enhancing sustainable agricultural productivity.

The Contrivance of Plant Growth Promoting Microbes to Mitigate Climate Change Impact in Agriculture

Combating the consequences of climate change is extremely important and critical in the context of feeding the world's population. Crop simulation models have been extensively studied recently to investigate the impact of climate change on agricultural productivity and food security. Drought and salinity are major environmental stresses that cause changes in the physiological, biochemical, and molecular processes in plants, resulting in significant crop productivity losses. Excessive use of chemicals has become a severe threat to human health and the environment. The use of beneficial microorganisms is an environmentally friendly method of increasing crop yield under environmental stress conditions. These microbes enhance plant growth through various mechanisms such as production of hormones, ACC deaminase, VOCs and EPS, and modulate hormone synthesis and other metabolites in plants. This review aims to decipher the effect of plant growth promoting bacteria (PGPB) on plant health under abiotic soil stresses associated with global climate change (viz., drought and salinity). The application of stress-resistant PGPB may not only help in the combating the effects of abiotic stressors, but also lead to mitigation of climate change. More thorough molecular level studies are needed in the future to assess their cumulative influence on plant development.

Seed Treatment With Systemic Fungicides: Time for Review

Pre-sowing seed treatment with systemic fungicides is a firmly entrenched practice for most agricultural crops worldwide. The treatment is intended to protect the crop against seed- and soil-borne diseases. In recent years, there is increasing evidence that fungicidal applications to manage diseases might inadvertently also affect non-target organisms, such as endophytes. Endophytes are ubiquitously present in plants and contribute to plant growth and development besides offering resistance to biotic and abiotic stresses. In seeds, endophytes may play a role in seed development, seed germination, seedling establishment and crop performance. In this paper, we review the recent literature on non-target effects of fungicidal applications on endophytic fungal community and discuss the possible consequences of indiscriminate seed treatment with systemic fungicide on seed endophytes. It is now well recognized that endophytes are ubiquitously present in all parts of the plant, including the seeds. They may be transmitted vertically from seed to seed as in many grasses and/or acquired horizontally from the soil and the environment. Though the origins and evolution of these organisms in plants are a matter of conjecture, numerous studies have shown that they symbiotically aid in plant growth and development, in nutrient acquisition as well in protecting the plants from abiotic and biotic stresses. Against this background, it is reasonable to assume that the use of systemic fungicides in seed treatment may not only affect the seed endophytes but also their attendant benefits to seedling growth and establishment. While there is evidence to indicate that fungicidal applications to manage plant diseases also affect foliar endophytes, there are only few studies that have documented the effect of seed treatment on seed-borne endophytes. Some of the convincing examples of the latter come from studies on the effect of fungicide application on rye grass seed endophyte AR37. More recently, experiments have shown that removal of seed endophytes by treatment with systemic fungicides leads to significant loss of seedling vigour and that such losses could be partially restored by enriching the seedlings with the lost endophytes. Put together, these studies reinforce the importance of seed endophytes to seedling growth and establishment and draw attention on how to trade the balance between the benefits of seed treatments and the direct and indirect costs incurred due to loss of endophytes. Among several approaches, use of reduced-risk fungicides and identifying fungicide-resistant endophytes are suggested to sustain the endophyte contribution to early seedling growth.

Endophyte roles in nutrient acquisition, root system architecture development and oxidative stress tolerance

Plants associate with communities of microbes (bacteria and fungi) that play critical roles in plant development, nutrient acquisition and oxidative stress tolerance. The major share of plant microbiota is endophytes which inhabit plant tissues and help them in various capacities. In this article, we have reviewed what is presently known with regard to how endophytic microbes interact with plants to modulate root development, branching, root hair formation and their implications in overall plant development. Endophytic microbes link the interactions of plants, rhizospheric microbes and soil to promote nutrient solubilization and further vectoring these nutrients to the plant roots making the soil-plant-microbe continuum. Further, plant roots internalize microbes and oxidatively extract nutrients from microbes in the rhizophagy cycle. The oxidative interactions between endophytes and plants result in the acquisition of nutrients by plants and are also instrumental in oxidative stress tolerance of plants. It is evident that plants actively cultivate microbes internally, on surfaces and in soils to acquire nutrients, modulate development and improve health. Understanding this continuum could be of greater significance in connecting endophytes with the hidden half of the plant that can also be harnessed in applied terms to enhance nutrient acquisition through the development of favourable root system architecture for sustainable production under stress conditions.

Multifaceted intervention of Bacillus spp. against salinity stress and Fusarium wilt in tomato

AIM

This study aimed to screen halotolerant Bacillus strains able to promote growth and protect tomato plants against salt stress and Fusarium wilt (Fusarium oxysporum f. sp. lycopersici).

METHODS AND RESULTS

We evaluated some halotolerant strains of Bacillus spp. (Bacillus velezensis (AP-3) and Bacillus spp. (AP-6, AP-85 and AP-100)) to promote growth of tomato plants grown under salinity stress conditions and to protect them against Fusarium wilt disease. Such strains had been previously selected among 154 bacterial strains through biochemical tests (siderophores and indoleacetic acid productions, cellulase and catalase activity, nitrogen fixation and phosphate solubilization) in the presence of 100-mmol l^-1 NaCl. Besides the above-mentioned strains, B. subtilis QST-713 (Serenade^TM ) was also evaluated. Compared to control plants, aboveground dry weight increased in plants inoculated with AP-6, AP-85, AP-3, AP-100 and QST-713 strains developed in the absence of salt stress. The same tendency occurred for root dry weight; however, AP-3 strain was more effective, promoting an increase of 163%, when compared to control. Chlorophyll index and height increased >40 and 53%, respectively, for all Bacillus strains. Saline stress reduced plant growth regardless of the presence of Bacillus. Height, stem diameter, and aboveground and root dry weights increased in plants treated with Bacillus strains grown under saline conditions when compared to control. Bacillus velezensis AP-3 reduced the severity of Fusarium wilt in tomato by 50% when compared to control.

CONCLUSION

Halotolerant Bacillus strains controlled tomato Fusarium wilt, increased growth as well as tolerance to salt stress.

SIGNIFICANCE AND IMPACT OF THE STUDY

We demonstrated the efficacy of halotolerant Bacillus strains to control Fusarium wilt and improve tomato growth. We also demonstrated that these Bacillus strains protect tomato plants against salt stress. Bacillus can be used in an eco-friendly way because they are considered Generally Recognized As Safe.

Isolation and screening of potassium solubilizing bacteria from saxicolous habitat and their impact on tomato growth in different soil types

Bacteria that solubilize nutrients in the soil are commonly used as bio-inoculants for promoting the growth of different crop species. However, the influence of potassium (K) solubilizing bacteria (KSB) originating from saxicolous habitat (rock-dwelling) on plant growth has not been frequently examined. In this study, we isolated KSB from saxicolous habitats and estimated their ability to produce plant growth hormone, organic acids, and siderophore that may facilitate plant growth. Fifteen culturable saxicolous bacterial isolates with varied K solubilizing ability were isolated from two sites. Of these, four potential K solubilizers were selected and identified by 16S rRNA gene sequencing. The four bacterial isolates resembled Bacillus subtilis, Bacillus cereus, Bacillus licheniformis, and Burkholderia cenocepacia and produced different organic acids, indole acetic acid, and siderophore under in vitro conditions. Potassium solubilization differed among the bacterial isolates and was significantly influenced by K sources. Inoculation of KSB improved the tomato plant growth parameters like plant height, leaf area, total root length, root/shoot ratio, and tissue K content in sterilized and unsterilized Alfisol, and Vertisol soils under greenhouse conditions. We also observed higher residual K content in the KSB inoculated post-harvest soils. Among the four KSB isolates screened, B. licheniformis and B. cenocepacia presents an excellent prospect as bio-inoculants for improving tomato growth in different soil types. Besides these, the enriched K content in the post-harvest soils may help the growth of subsequent crops in sustainable agriculture.

Microbial Diversity of Psychrotolerant Bacteria Isolated from Wild Flora of Andes Mountains and Patagonia of Chile towards the Selection of Plant Growth-Promoting Bacterial Consortia to Alleviate Cold Stress in Plants

Cold stress decreases the growth and productivity of agricultural crops. Psychrotolerant plant growth-promoting bacteria (PGPB) may protect and promote plant growth at low temperatures. The aims of this study were to isolate and characterize psychrotolerant PGPB from wild flora of Andes Mountains and Patagonia of Chile and to formulate PGPB consortia. Psychrotolerant strains were isolated from 11 wild plants (rhizosphere and phyllosphere) during winter of 2015. For the first time, bacteria associated with Calycera, Orites, and Chusquea plant genera were reported. More than 50% of the 130 isolates showed ≥33% bacterial cell survival at temperatures below zero. Seventy strains of Pseudomonas, Curtobacterium, Janthinobacterium, Stenotrophomonas, Serratia, Brevundimonas, Xanthomonas, Frondihabitans, Arthrobacter, Pseudarthrobacter, Paenarthrobacter, Brachybacterium, Clavibacter, Sporosarcina, Bacillus, Solibacillus, Flavobacterium, and Pedobacter genera were identified by 16S rRNA gene sequence analyses. Ten strains were selected based on psychrotolerance, auxin production, phosphate solubilization, presence of nifH (nitrogenase reductase) and acdS (1-aminocyclopropane-1-carboxylate (ACC) deaminase) genes, and anti-phytopathogenic activities. Two of the three bacterial consortia formulated promoted tomato plant growth under normal and cold stress conditions. The bacterial consortium composed of Pseudomonas sp. TmR5a & Curtobacterium sp. BmP22c that possesses ACC deaminase and ice recrystallization inhibition activities is a promising candidate for future cold stress studies.

Altered bacteria community dominance reduces tolerance to resident fungus and seed to seedling growth performance in maize (Zea mays L. var. DKB 177)

Seeds are reservoirs of beneficial and harmful microorganism that modulates plant growth and health. Here, we access seed to seedling bacteriome assembly modified by seed-disinfection and the underlined effect over maize germination performance and root-seedlings microbial colonization. Seed-disinfection was performed with sodium hypochlorite (1.25 %, 30 min), resulting in a reduction of the cultivable-dependent fraction of seed-borne bacteria population, but not significantly detected by real-time PCR, microscopy, and biochemical analysis of the roots on germinated seeds. 16S rRNA sequencing revealed that bacteriome of non-germinated seeds and roots of 5-d germinated seeds exhibited similar diversity and did not differ in the structure concerning seed-disinfection. On the other hand, the relative abundance reduction of the genera f_Enterobacteriaceae_922761 (unassigned genus), Azospirillum, and Acinetobacter in disinfected-seed prior germination seems to display changes in prominence of several new taxa in the roots of germinated seeds. Interestingly, this bacteriome community rebuilt negatively affected the germination speed and growth of maize plantlets. Additionally, bacteriome re-shape increased the maize var. DKB 177 susceptible to the seed-borne plant pathogen Penicillium sp. Such changes in the natural seed-borne composition removed the natural barrier, increasing susceptibility to pathogens, impairing disinfected seeds to germinate, and develop. We conclude that bacteria borne in seeds modulate the relative abundance of taxa colonizing emerged roots, promote germination, seedling growth, and protect the maize against fungal pathogens.

Salt-Tolerant Plant Growth Promoting Rhizobacteria for Enhancing Crop Productivity of Saline Soils

Soil salinity has emerged as a serious issue for global food security. It is estimated that currently about 62 million hectares or 20 percent of the world's irrigated land is affected by salinity. The deposition of an excess amount of soluble salt in cultivable land directly affects crop yields. The uptake of high amount of salt inhibits diverse physiological and metabolic processes of plants even impacting their survival. The conventional methods of reclamation of saline soil which involve scraping, flushing, leaching or adding an amendment (e.g., gypsum, CaCl2, etc.) are of limited success and also adversely affect the agro-ecosystems. In this context, developing sustainable methods which increase the productivity of saline soil without harming the environment are necessary. Since long, breeding of salt-tolerant plants and development of salt-resistant crop varieties have also been tried, but these and aforesaid conventional approaches are not able to solve the problem. Salt tolerance and dependence are the characteristics of some microbes. Salt-tolerant microbes can survive in osmotic and ionic stress. Various genera of salt-tolerant plant growth promoting rhizobacteria (ST-PGPR) have been isolated from extreme alkaline, saline, and sodic soils. Many of them are also known to mitigate various biotic and abiotic stresses in plants. In the last few years, potential PGPR enhancing the productivity of plants facing salt-stress have been researched upon suggesting that ST-PGPR can be exploited for the reclamation of saline agro-ecosystems. In this review, ST-PGPR and their potential in enhancing the productivity of saline agro-ecosystems will be discussed. Apart from this, PGPR mediated mechanisms of salt tolerance in different crop plants and future research trends of using ST-PGPR for reclamation of saline soils will also be highlighted.

Review: Endophytic microbes and their potential applications in crop management

Endophytes are microbes (mostly bacteria and fungi) present asymptomatically in plants. Endophytic microbes are often functional in that they may carry nutrients from the soil into plants, modulate plant development, increase stress tolerance of plants, suppress virulence in pathogens, increase disease resistance in plants, and suppress development of competitor plant species. Endophytic microbes have been shown to: (i) obtain nutrients in soils and transfer nutrients to plants in the rhizophagy cycle and other nutrient-transfer symbioses; (ii) increase plant growth and development; (iii) reduce oxidative stress of hosts; (iv) protect plants from disease; (v) deter feeding by herbivores; and (vi) suppress growth of competitor plant species. Because of the effective functions of endophytic microbes, we suggest that endophytic microbes may significantly reduce use of agrochemicals (fertilizers, fungicides, insecticides, and herbicides) in the cultivation of crop plants. The loss of endophytic microbes from crop plants during domestication and long-term cultivation could be remedied by transfer of endophytes from wild relatives of crops to crop species. Increasing atmospheric carbon dioxide levels could reduce the efficiency of the rhizophagy cycle due to repression of reactive oxygen used to extract nutrients from microbes in roots. © 2019 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

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.

Indigenous endophytic seed bacteria promote seedling development and defend against fungal disease in browntop millet (Urochloa ramosa L.)

AIMS

This study was conducted to investigate indigenous seed endophyte effects on browntop millet seedling development. We report that seed-inhabiting bacterial endophytes are responsible for promoting seedling development, including stimulation of root hair formation, increasing root and shoot length growth and increasing photosynthetic pigment content of seedlings. Bacterial endophytes also improved resistance of seedlings to disease.

METHODS AND RESULTS

A total of four endophytic bacteria were isolated from surface-sterilized seeds and identified by 16S rDNA sequencing as Curtobacterium sp. (M1), Microbacterium sp. (M2), Methylobacterium sp. (M3) and Bacillus amyloliquefaciens (M4). Removal of bacteria with streptomycin treatment from the seeds compromised seedling growth and development. When endophytes were reinoculated onto seeds, seedlings recovered normal development. Strains M3 and M4 were found to be most potent in promoting growth of seedlings. Bacteria were found to produce auxin, solubilize phosphate and inhibit fungal pathogens. Significant protection of seedlings from Fusarium infection was found using strain M4 in microcosm assays. The antifungal lipopeptide genes for surfactin and iturin were detected in M4; culture extracts of M4 showed a positive drop collapse result for surfactins.

CONCLUSIONS

This study demonstrates that browntop millet seeds vector indigenous endophytes that are responsible for modulation of seedling development and protection of seedlings from fungal disease.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study is significant and original in that it is the first report of seed-inhabiting endophytes of browntop millet that influence seedling development and function in defence against soilborne pathogens. This study suggests that conservation and management of seed-vectored endophytes may be important in development of more sustainable agricultural practices.