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Aims Soil salinity is a huge obstacle in crop production worldwide. Saline soil can reduce active chemical contents in medicinal plants of the Leguminosae family through crippled normal nodule function. Intensive efforts are underway to improve yield and medicinal value of leguminous herbs under salt stress condition by using benign microbes. Here, an attempt was made to explore the salt-tolerant bacteria associated with rhizosphere of fenugreek plant (Trigonella foenum-graecum L.) and to evaluate their impact on host plant growth and metabolite of pharmaceutical importance. Methods and results A salt-tolerant plant growth promoting rhizobacterial (PGPR) strain Priestia endophytica SK1 isolated from fenugreek rhizospheric soil, which increased biomass and metabolite content in plants grown under saline stress. SK1 bacterial application induced nodule formation and enhanced nitrogen and phosphorus content under salt (100 mM NaCl) stress as compared to control plants. H2O2 production and lipid peroxidation as a measure of stress were observed high in control plants, while a reduction in these parameters was observed in plants inoculated with SK1. In addition, a significant effect was found on the phenolic compounds and trigonelline content in fenugreek plant inoculated with SK1 bacterium. An increased trigonelline content of about 54% over uninoculated control was recorded under salt stress. Conclusion The results of this study revealed that the application of salt-tolerant PGPR strain P. endophytica SK1 induced nitrogen fixation machinery that leads to alleviate salt stress and improved the biosynthesis of trigonelline content in fenugreek. Significance of the study This study extends our understanding on the significance of rhizosphere microbiome and their beneficial role in plant health under environmental stress to promote agro-eco-farming practices.

Tomato is an important nutritional vegetable crop and its nutrient contents are affected by both biotic and abiotic stresses. The main objective of this study was to determine the effect of seed biopriming with Trichoderma pseudokoningii BHUR2 and vermiwash treatment on nutrient content of tomato and defense response against Sclerotium rolfsii under heat stress condition. The combined application of T. pseudokoningii BHUR2 and vermiwash increased fresh weight of root (4.8-fold) and shoot (5.8-fold), dry weight of root (6.9-fold) and shoot (6.4-fold) and number of fruits per plant (4.2-fold) as compared to control under S. rolfsii inoculated condition. Plants treated with T. pseudokoningii BHUR2 and vermiwash exhibited higher defense response against S. rolfsii, mediated by higher activity of superoxide dismutase (3.57-fold), peroxidase (2.05-fold) and phenylalanine ammonia lyase (2.98-fold) enzymes and accumulation of total phenol content (5.35-fold) as compared to control plants. In addition, combined treatment was found to have a positive impact on nutritional status (N, P, K and Ca and lycopene, total soluble sugar and total protein) in tomato fruit. These results suggest potential of T. pseudokoningii BHUR2 and vermiwash in enhancing tomato immunity against S. rolfsii under heat stress condition, which was due to (1) induction in the antioxidant activity and phenylpropanoid pathway, which minimize oxidative damage and reduce pathogen infection and (2) significant improvement in nutrient content leads to better plant growth. The formulation of Trichoderma BHUR2 can be used for field application to mitigate heat stress in plants.

Microorganisms are an important component of the ecosystem and have an enormous impact on human lives. Moreover, microorganisms are considered to have desirable effects on other co-existing species in a variety of habitats, such as agriculture and industries. In this way, they also have enormous environmental applications. Hence, collections of microorganisms with specific traits are a crucial step in developing new technologies to harness the microbial potential. Microbial culture collections (MCCs) are a repository for the preservation of a large variety of microbial species distributed throughout the world. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are vital for the safeguarding and circulation of biological resources, as well as for the progress of the life sciences. Ex situ conservation of microorganisms tagged with specific traits in the collections is the crucial step in developing new technologies to harness their potential. Type strains are mainly used in taxonomic study, whereas reference strains are used for agricultural, biotechnological, pharmaceutical research and commercial work. Despite the tremendous potential in microbiological research, little effort has been made in the true sense to harness the potential of conserved microorganisms. This review highlights (1) the importance of available global microbial collections for man and (2) the use of these resources in different research and applications in agriculture, biotechnology, and industry. In addition, an extensive literature survey was carried out on preserved microorganisms from different collection centres using the Web of Science (WoS) and SCOPUS. This review also emphasizes knowledge gaps and future perspectives. Finally, this study provides a critical analysis of the current and future roles of microorganisms available in culture collections for different sustainable agricultural and industrial applications. This work highlights target-specific potential microbial strains that have multiple important metabolic and genetic traits for future research and use.

Incessant release of nitrile group of compounds such as cyanides into agricultural land through industrial effluents and excessive use of nitrile pesticides has resulted in increased nitrile pollution. Release of nitrile compounds (NCs) as plant root exudates is also contributing to the problem. The released NCs interact with soil elements and persists for a long time. Persistent higher concentration of NCs in soil cause toxicity to beneficial microflora and affect crop productivity. The NCs can cause more problems to human health if they reach groundwater and enter the food chain. Nitrile degradation by soil bacteria can be a solution to the problem if thoroughly exploited. However, the impact of such bacteria in plant and soil environments is still not properly explored. Plant growth-promoting rhizobacteria (PGPR) with nitrilase activity has recently gained attention as potential solution to address the problem. This paper reviews the core issue of nitrile pollution in soil and the prospects of application of nitrile degrading bacteria for soil remediation, soil health improvement and plant growth promotion in nitrile-polluted soils. The possible mechanisms of PGPR that can be exploited to degrade NCs, converting them into plant useful compounds and synthesis of the phytohormone IAA from degraded NCs are also discussed at length.

Soil salinity causes severe environmental stress that affects agriculture production and food security throughout the world. Salt-tolerant plant-growth-promoting rhizobacteria (PGPR) and nitric oxide (NO), a distinctive signaling molecule, can synergistically assist in the alleviation of abiotic stresses and plant growth promotion, but the mechanism by which this happens is still not well known. In the present study, in a potential salt-tolerant rhizobacteria strain, ASN-1, growth up to 15% NaCl concentration was achieved with sugarcane rhizosphere soil. Based on 16S-rRNA gene sequencing analysis, the strain ASN-1 was identified as a Bacillus xiamenensis. Strain ASN-1 exhibits multiple plant-growth-promoting attributes, such as the production of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylate deaminase, siderophores, HCN, ammonia, and exopolysaccharides as well as solubilized phosphate solubilization. Biofilm formation showed that NO enhanced the biofilm and root colonization capacity of the PGPR strain ASN-1 with host plants, evidenced by scanning electron microscopy. The greenhouse study showed that, among the different treatments, the combined application of PGPR and sodium nitroprusside (SNP) as an NO donor significantly (p ≤ 0.05) enhanced sugarcane plant growth by maintaining the relative water content, electrolyte leakage, gas exchange parameters, osmolytes, and Na+/K+ ratio. Furthermore, PGPR and SNP fertilization reduced the salinity-induced oxidative stress in plants by modulating the antioxidant enzyme activities and stress-related gene expression. Thus, it is believed that the acquisition of advanced information about the synergistic effect of salt-tolerant PGPR and NO fertilization will reduce the use of harmful chemicals and aid in eco-friendly sustainable agricultural production under salt stress conditions.

Cereals are important crops and are exposed to various types of environmental stresses that affect the overall growth and yield. Among the various abiotic stresses, salt stress is a major environmental factor that influences the genetic, physiological, and biochemical responses of cereal crops. Epigenetic regulation which includes DNA methylation, histone modification, and chromatin remodelling plays an important role in salt stress tolerance. Recent studies in rice genomics have highlighted that the epigenetic changes are heritable and therefore can be considered as molecular signatures. An epigenetic mechanism under salinity induces phenotypic responses involving modulations in gene expression. Association between histone modification and altered DNA methylation patterns and differential gene expression has been evidenced for salt sensitivity in rice and other cereal crops. In addition, epigenetics also creates stress memory that helps the plant to better combat future stress exposure. In the present review, we have discussed epigenetic influences in stress tolerance, adaptation, and evolution processes. Understanding the epigenetic regulation of salinity could help for designing salt-tolerant varieties leading to improved crop productivity.

Fusarium wilt is one of the major diseases of tomato causing extensive loss of production. Exploration of agriculturally important microbes (AIMs) for management of the tomato wilt is an ecofriendly and cost effective approach. In the present study, a total 30 Trichoderma and 30 bacterial isolates were screened in the laboratory for their biocontrol activity against Fusarium oxysporum f.sp. lycopersici (FOL). Out of all the isolates tested, Trichoderma asperellum BHU P-1 and Ochrobactrum sp. BHU PB-1 were found to show maximum inhibition of FOL in dual culture assay. Both the microbes also exhibited plant growth promoting activities such as phosphate solubilisation, production of siderophore, hydrogen cyanide (HCN), indole acetic acid (IAA) and protease activity. These microbes could be evaluated further in greenhouse and field studies for their potential use in management of Fusarium wilt of tomato.

To provide food security with quality crops for exponentially growing population brought intense pressure on the limited land and natural resources among developing countries. Abiotic stresses such as continuously rising temperature as consequences of global warming is adding pressure to existing problems by adversely affecting crop productivity through physiological changes in plants. Hence there is need of qualitatively potential vegetable crops that can withstand changing environmental conditions such as Okra (Abelmoschus spp.) holding high level of nutrients along with economic importance. But requirement of high temperature and humidity for its cultivation make the plant prone to several phytopathogens that ultimately leads to severe qualitative and quantitative losses depending upon the plant growth stage getting affected. Due to the unenviable problems of chemical fertilizers, biocontrol agents were applied as auxiliary treatments either single or in combination that possess fewer consequences on the environment. But due to increasing environmental and soil temperature, activities of these formulations are getting hindered. Therefore, there is an urgent requirement to procure high temperature stress tolerant strains along with antagonistic and plant growth promoting abilities. In the current study, we mainly focused on isolation of high temperature tolerant Trichoderma harzianum (BHU P4) strain with antagonistic abilities against fungal pathogen Sclerotium rolfsii causing collar rot disease. The strain was also studied for plant growth promoting attributes in okra plant which resulted in increased fresh weight, dry weight, chlorophyll content and nutrient content in comparison to control and pathogen challenged plants. This study was associated with an improvement in the level of total phenol, SOD, PO and PAL enzymes in order to regulate the host defense mechanism against its confrontation with S. rolfsii.

Based on natural and anthropogenic activities, the soil quality has depleted gradually which is also mediated through unpredictably changed environmental conditions. As a consequence, a challenge has been raised before farmers and nations to compensate the degraded soil quality. To replenish the soil quality, farmers deploy synthetic fertilizer which is an unsustainable practice and further lead conditions worse by the diminished biological activity, increased level of toxicity, decreased fertility, etc. As a comparatively safe and sustainable alternative, PGPRs have been characterized as they could always assist plants against various challenges like nutrient unavailability, abiotic stresses, and pathogens. Many of those PGPRs which have been studied for their beneficial impacts are now used on a commercial scale for alleviating abiotic and biotic stresses of crop plants. Some of the PGPRs with wonderful ex situ and in situ performances are Azospirillum brasilense, Azospirillum lipoferum, Bacillus, Pseudomonas, Acinetobacter, Alcaligenes faecalis, Stenotrophomonas, Pseudomonas, Rahnella, Pseudomonas fluorescens, Bacillus megaterium, Bacillus licheniformis, Proteus mirabilis, Achromobacter xylosoxidans, Gluconoacetobacter diazotrophicus, Azoarcus, Pseudomonas migulae, Brachybacterium saurashtrense, Brevibacterium casei, Haererohalobacter, and many more which have surely assisted plant including a list of Arabidopsis, maize, wheat, potato, tomato, capsicum, etc. This chapter unfolds important mechanisms and strategies used by PGPRs to help crop plant cope up the various biotic and abiotic stresses and increase soil and plant health.

Contaminated soil has adverse effects on legume symbiosis, which lead to disturbance in nitrogen metabolism in plants. Although several studies have been performed on response of biological nitrogen fixation (BNF) under stress condition, less is known about how leguminous plants adjust their BNF process under contaminated soil. Fenugreek (Trigonella foenum-graecum) is an annual plant belonging to legume family and majorly grown in Northern region of India for its medicinal property. Northern region of India is mainly affected with dynamic climate that ultimately cause adverse effect on plant cultivation. In addition, due to many functioning industries in this region, nearby agricultural lands are affected with their toxic effluents. These effluents contaminate agricultural soil with heavy metals and salts, where leguminous plants fail to perform rhizobia symbiosis. However, plant releases more number of antioxidants, flavonoids, or other phenolic compounds to cope with such a type of soil stress. In the present chapter, fenugreek plant property and its rhizobial symbiosis are discussed here. Some case studies also mentioned on role of exogenous flavonoids in alleviation of soil stress effects on nodule formation. The present study suggests the use of flavonoid compounds as plant biostimulants for improving BNF process in legume plant under soil stress conditions and also explores new study in this direction.

The soil microbial community hugely affects the growth and development of the plants through direct or indirect interactions. The rhizospheric microbial community dwelling in the soil are major drivers of this phenomenon. Manipulation of soil microbial population and community through various treatments of an array of beneficial microbes such as plant growth-promoting rhizobacteria, plant growth-promoting fungi, endophytic bacteria, biocontrol agents, etc. helps in alleviating various abiotic and biotic stresses of the plants. This, in turn, leads to the achievement of the yield which is close to the potential yield of the crop. Apart from increasing the yield of the crop, some of the beneficial microbes also enhance the nutrient content in the soil and availability of certain minerals to the plants eventually leading to conservation of soil health. Thus, manipulation of plant–soil microbiome paves the way for sustainable and green agriculture without imparting excessive monetary expenses, thereby creating increased crop production and embellishment of soil health. This chapter will so focus on the strategies and methods that are adopted to manipulate the plant–soil microbiome interactions, various mechanisms that are involved in the interactions, and the impact of this technology on the plant and soil.

Biological nitrogen fixation (BNF) is a sustainable approach to reduce negative effects of chemical N fertilizers on ecosystem. Therefore, BNF has gained special attention in researchers for enhancing its effectiveness among different crop plants. The genetic mutation approach in bacterial spp. towards efficient symbiosis and plant growth promotion is an attractive strategy nowadays. In addition, positive mutants of plant growth promoting rhizobacterial (PGPR) strains could survive under harsh conditions and promote plant growth also. The objectives of the present chapter are to highlight the basic mechanisms of induced mutation in bacteria and applied aspects of these mutated bacteria for improving nitrogen-fixing abilities in plants.

Microbial volatile organic compounds (mVOCs) have great potential in plant ecophysiology, yet the role of belowground VOCs in plant stress management remains largely obscure. Analysis of biocontrol producing VOCs into the soil allow detailed insight into their interaction with soil borne pathogens for plant disease management. A root interaction trial was set up to evaluate the effects of VOCs released from Trichoderma viride BHU-V2 on soil-inhabiting fungal pathogen and okra plant growth. VOCs released into soil by T. viride BHU-V2 inhibited the growth of collar rot pathogen, Sclerotium rolfsii. Okra plants responded to VOCs by increasing the root growth (lateral roots) and total biomass content. VOCs exposure increased defense mechanism in okra plants by inducing different enzyme activities i.e. chitinase (0.89 fold), β-1,3-glucanase (0.42 fold), peroxidase (0.29 fold), polyphenol oxidase (0.33 fold) and phenylalanine lyase (0.7 fold) when inoculated with S. rolfsii. In addition, T. viride BHU-V2 secreted VOCs reduced lipid peroxidation and cell death in okra plants under pathogen inoculated condition. GC/MS analysis of VOCs blend revealed that T. viride BHU-V2 produced more number of antifungal compounds in soil medium as compared to standard medium. Based on the above observations it is concluded that okra plant roots perceive VOCs secreted by T. viride BHU-V2 into soil that involved in induction of plant defense system against S. rolfsii. In an ecological context, the findings reveal that belowground microbial VOCs may play an important role in stress signaling mechanism to interact with plants.

Salt tolerant bacteria can be helpful in improving a plant’s tolerance to salinity. Although plant–bacteria interactions in response to salt stress have been characterized, the precise molecular mechanisms by which bacterial inoculation alleviates salt stress in plants are still poorly explored. In the present study, we aimed to determine the role of a salt-tolerant plant growth-promoting rhizobacteria (PGPR) Sphingobacterium BHU-AV3 for improving salt tolerance in tomato through investigating the physiological responses of tomato roots and leaves under salinity stress. Tomato plants inoculated with BHU-AV3 and challenged with 200 mM NaCl exhibited less senescence, positively correlated with the maintenance of ion balance, lowered reactive oxygen species (ROS), and increased proline content compared to the non-inoculated plants. BHU-AV3-inoculated plant leaves were less affected by oxidative stress, as evident from a reduction in superoxide contents, cell death, and lipid peroxidation. The reduction in ROS level was associated with the increased antioxidant enzyme activities along with multiple-isoform expression [peroxidase (POD), polyphenol oxidase (PPO), and superoxide dismutase (SOD)] in plant roots. Additionally, BHU-AV3 inoculation induced the expression of proteins involved in (i) energy production [ATP synthase], (ii) carbohydrate metabolism (enolase), (iii) thiamine biosynthesis protein, (iv) translation protein (elongation factor 1 alpha), and the antioxidant defense system (catalase) in tomato roots. These findings have provided insight into the molecular mechanisms of bacteria-mediated alleviation of salt stress in plants. From the study, we can conclude that BHU-AV3 inoculation effectively induces antioxidant systems and energy metabolism in tomato roots, which leads to whole plant protection during salt stress through induced systemic tolerance.

Microbial biofilm is a new emerging subject for microbiologists to work in the areas of environment, industry, agriculture, and health. Biofilms enhance the proliferation and colonization of microbes on surface and protect cells in an adverse environment. The potential of microbes surrounded by biofilms has recently been realized for bioremediation processes. The mutually beneficial interaction of multiple microorganisms in biofilms attracts attention toward xenobiotics and their uses in industrial plants to degrade pollutants. Microbial biofilms are using in different bioreactors and biofilters for pollutant degradation on a large scale. Although limited information is are available on bioremediation through microbial biofilms, this chapter presents the fundamental aspects of biofilms and their application in the bioremediation field. A better understanding of the role of microbial mechanisms in pollutant tolerance and their degradation can be beneficial for bioremediation strategies. Understanding the mechanisms and genes involved in biofilm formation will help to develop new strategies for bioremediation.

Sclerotium rolfsii is a polyphagous pathogen, and its management is quite difficult and uneconomical owing to its wide host range and long-term survival in the form of hard resting structure, i.e., sclerotia. The pathogen is a threat to most of the agricultural crops as it incurs heavy yield losses. Chemical control, though, provides quick results, but it evokes concern relating to human health and is non-eco-friendly. Indiscriminate use of chemical fungicides leads to accretion of harmful chemical residues on the targeted crop, leading to serious health issues of the consumers. Biological control of phytopathogens has emerged as an attractive alternative to chemical control. Application of antagonistic microbes is considered as one of the potential management strategies in integrated management approach owing to their eco-friendly nature. Among them, Trichoderma species has been recognized as a potent biocontrol agent and is widely applied for the management of soilborne pathogens. A number of Trichoderma-based formulations, viz. Soilguard, Trichodex, and Trichojet, are commercially available in the market. Thus, biological management is a perfect alternative for chemical control as it ascertains food security in an ecologically safe and sound manner. Being a very popular biocontrol agent, Trichoderma spp. has a tremendous ability in the management of various diseases induced by S. rolfsii. Several researches carried out in the past are an explicit example of this. So the need of the hour is higher popularization of Trichoderma spp. for the efficient management of S. rolfsii in an eco-friendly manner.

Trichoderma is a genetically diverse group of fungi present in different ecological niches with multiple capabilities. Most of the Trichoderma spp. are reported as plant growth promoters and efficient biocontrol agents against various biotic and biotic stresses. Besides that genus Trichoderma is also utilized for bioremediation of heavy metal contamination, pesticide residue degradation, and industrial purposes for food, beverages, nanoparticles, and pharmaceuticals. These fungal species produce a vast variety of extracellular enzymes including cellulase, which play a key role in the degradation of complex polysaccharides and other organic compounds. The application of these enzymes into industries has been an economically and environmentally sustainable approach for producing high-quality products. As Trichoderma genomic sequences are now available in the public domain, it can be explored to search its wider applicability in the scientific arena. This chapter presents an overview of the application of Trichoderma beyond the agriculture areas like food industries, pharmaceuticals, beverages, bioremediation, and nanotechnology.

Soil salinity is a major limiting factor for crop productivity worldwide and is continuously increasing owing to climate change. A wide range of studies and practices have been performed to induce salt tolerance mechanisms in plants, but their result in crop improvement has been limited due to lack of time and money. In the current scenario, there is increasing attention towards habitat-imposed plant stress tolerance driven by plant-associated microbes, either rhizospheric and/or endophytic. These microbes play a key role in protecting plants against various environmental stresses. Therefore, the use of plant growth-promoting microbes in agriculture is a low-cost and eco-friendly technology to enhance crop productivity in saline areas. In the present review, the authors describe the functionality of endophytic bacteria and their modes of action to enhance salinity tolerance in plants, with special reference to osmotic and ionic stress management. There is concrete evidence that endophytic bacteria serve host functions, such as improving osmolytes, anti-oxidant and phytohormonal signaling and enhancing plant nutrient uptake efficiency. More research on endophytes has enabled us to gain insights into the mechanism of colonization and their interactions with plants. With this information in mind, the authors tried to solve the following questions: (1) how do benign endophytes ameliorate salt stress in plants? (2) What type of physiological changes incur in plants under salt stress conditions? And (3), what type of determinants produced by endophytes will be helpful in plant growth promotion under salt stress?

Plant growth promoting rhizobacteria (PGPR) have been described for sustainable agriculture practices as being a vital agent for abiotic and biotic stress mitigation and growth promotion in plants. In the present research, the authors emphasize the role of drought tolerant PGPR namely, Pseudomonas simiae strain AU, in protection of soybean plants by modulating the gene expression profile and phytohormone biosynthesis responsible for drought tolerance in plants. The gene expression analysis confirmed the involvement of transcription factors (DREB/EREB), osmoprotectants (P5CS, GOLS), and water transporters (PIP & TIP), as these genes were up-regulated in P. simiae AU-inoculated plants leading to drought tolerance. In addition, enhanced production of abscisic acid (ABA) and salicylic acid (SA) hormones and reduction of ethylene emission, associated with promoting drought tolerance, was observed in bacterial-inoculated plants in comparison to non-inoculated plants. Higher proline and total soluble sugar contents in AU-inoculated soybean plants also contributed to increased tolerance to drought stress. Overall, P. simiae AU mediated drought-induced expression profiles of stress genes and plant hormones were determined in soybean plants.