Phylogenetic analysis of halophyte‐associated rhizobacteria and effect of halotolerant and halophilic phosphate‐solubilizing biofertilizers on maize growth under salinity stress conditions

Exploring Halophiles for Reclamation of Saline Soils: Biotechnological Interventions for Sustainable Agriculture

Soil salinization is a major constraint on agricultural productivity, particularly in arid and semi-arid regions where limited rainfall cannot wash salts from plant root zones. This leads to disruptions in water uptake, ion balance, photosynthesis, respiration, nutrient absorption, hormone regulation and rhizosphere microbiome disturbances in plants. Chemical and biological methods can help mitigate soil salinity, but biological approaches, like using halophytes and salt-tolerant microorganisms, are preferred for environmental sustainability. Halophytes, however, represent only about 1% of flora and are habitat specific, so halophilic plant growth-promoting (PGP) microbes have emerged as a key eco-friendly solution. Halophilic PGP bacteria have shown promise in remediating saline soils, enhancing fertility and boosting crop resilience by inducing salinity tolerance (IST) and promoting plant growth traits. In the era of modern agriculture where chemical inputs are at their peak of application rendering the soil infertile, halophilic PGP bacteria represent a promising, sustainable approach to support food security, aligning with Sustainable Development Goals for zero hunger.

Transformative strategies for saline soil restoration: Harnessing halotolerant microorganisms and advanced technologies

Soil salinity is a critical global challenge that severely impairs crop productivity and soil health by disrupting water uptake, nutrient acquisition, and ionic balance in plants, thereby posing a significant threat to food security. This review underscores innovative strategies to mitigate salinity stress, focusing on the pivotal role of halotolerant microorganisms and their synergistic interactions with plants. Halotolerant microorganisms enhance plant resilience through diverse mechanisms under salinity, including exopolysaccharide production, sodium sequestration, and phytohormone regulation. It improves ionic balance, nutrient uptake, and root development, facilitated by osmoregulatory and genetic adaptations. In this discussion, we explored emerging technologies, including genome editing (e.g., CRISPR-Cas9), synthetic biology, and advanced omics-based tools such as metagenomics and metatranscriptomics. These cutting-edge approaches offer profound insights into microbial diversity and their functional adaptations to saline environments. By leveraging these technologies, it is possible to design targeted bioremediation strategies through the customization of microbial functionalities to address specific environmental challenges effectively. Advanced methodologies, such as microbial volatile organic compounds (mVOCs), nanotechnology, and stress-tolerant microbial consortia, significantly enhance plant stress tolerance and facilitate soil restoration. Moreover, integrating digital technologies, including machine learning and artificial intelligence (AI), optimizes bioremediation processes by providing precise, scalable, and adaptable solutions tailored to diverse agricultural ecosystems. The synergistic application of halotolerant microbe-mediated approaches with advanced biotechnological and digital innovations presents a transformative strategy for saline soil restoration. Future research should focus on harmonizing these technologies and methodologies to maximize plant-microbe interactions and establish resilient, sustainable agricultural systems.

Halotolerant Enterobacter asburiae A103 isolated from the halophyte Salix linearistipularis: Genomic analysis and growth-promoting effects on Medicago sativa under alkali stress

Soil salinization negatively affects plant growth and threatens food security. Halotolerant plant growth-promoting bacteria (PGPB) can alleviate salt stress in plants via diverse mechanisms. In the present study, we isolated salt-tolerant bacteria with phosphate-solubilizing abilities from the rhizosphere of Salix linearistipularis, a halophyte distributed in saline-alkali soils. Strain A103 showed high phosphate solubilization activity and was identified as Enterobacter asburiae based on genome analysis. In addition, it can produce indole-3-acetic acid (IAA), siderophores, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. Genome mining has also revealed the presence of several functional genes involved in the promotion of plant growth. Inoculation with A103 markedly improved alfalfa growth in the presence of 100 mM NaHCO3. Under alkali stress, the shoot and root dry weights after bacterial inoculation improved by 42.9 % and 21.9 %, respectively. Meanwhile, there was a 35.9-37.1 % increase in the shoot and root lengths after treatment with A103 compared to the NaHCO3-treated group. Soluble sugar content, peroxidase and catalase activities increased in A103-inoculated alfalfa under alkaline stress. A significant decrease in the malondialdehyde content was observed after treatment with strain A103. Metabolomic analysis indicated that strain A103 positively regulated alkali tolerance in alfalfa through the accumulation of metabolites, such as homocarnosine, panthenol, and sorbitol, which could reduce oxidative damage and act as osmolytes. These results suggest that halophytes are valuable resources for bioprospecting halotolerant beneficial bacteria and that the application of halotolerant growth-promoting bacteria is a natural and efficient strategy for developing sustainable agriculture.

Employing Genomic Tools to Explore the Molecular Mechanisms behind the Enhancement of Plant Growth and Stress Resilience Facilitated by a Burkholderia Rhizobacterial Strain

The rhizobacterial strain BJ3 showed 16S rDNA sequence similarity to species within the Burkholderia genus. Its complete genome sequence revealed a 97% match with Burkholderia contaminans and uncovered gene clusters essential for plant-growth-promoting traits (PGPTs). These clusters include genes responsible for producing indole acetic acid (IAA), osmolytes, non-ribosomal peptides (NRPS), volatile organic compounds (VOCs), siderophores, lipopolysaccharides, hydrolytic enzymes, and spermidine. Additionally, the genome contains genes for nitrogen fixation and phosphate solubilization, as well as a gene encoding 1-aminocyclopropane-1-carboxylate (ACC) deaminase. The treatment with BJ3 enhanced root architecture, boosted vegetative growth, and accelerated early flowering in Arabidopsis. Treated seedlings also showed increased lignin production and antioxidant capabilities, as well as notably increased tolerance to water deficit and high salinity. An RNA-seq transcriptome analysis indicated that BJ3 treatment significantly activated genes related to immunity induction, hormone signaling, and vegetative growth. It specifically activated genes involved in the production of auxin, ethylene, and salicylic acid (SA), as well as genes involved in the synthesis of defense compounds like glucosinolates, camalexin, and terpenoids. The expression of AP2/ERF transcription factors was markedly increased. These findings highlight BJ3's potential to produce various bioactive metabolites and its ability to activate auxin, ethylene, and SA signaling in Arabidopsis, positioning it as a new Burkholderia strain that could significantly improve plant growth, stress resilience, and immune function.

Extremophiles and their expanding biotechnological applications

Microbial life is not restricted to any particular setting. Over the past several decades, it has been evident that microbial populations can exist in a wide range of environments, including those with extremes in temperature, pressure, salinity, and pH. Bacteria and Archaea are the two most reported types of microbes that can sustain in extreme environments, such as hot springs, ice caves, acid drainage, and salt marshes. Some can even grow in toxic waste, organic solvents, and heavy metals. These microbes are called extremophiles. There exist certain microorganisms that are found capable of thriving in two or more extreme physiological conditions simultaneously, and are regarded as polyextremophiles. Extremophiles possess several physiological and molecular adaptations including production of extremolytes, ice nucleating proteins, pigments, extremozymes and exopolysaccharides. These metabolites are used in many biotechnological industries for making biofuels, developing new medicines, food additives, cryoprotective agents etc. Further, the study of extremophiles holds great significance in astrobiology. The current review summarizes the diversity of microorganisms inhabiting challenging environments and the biotechnological and therapeutic applications of the active metabolites obtained as a response to stress conditions. Bioprospection of extremophiles provides a progressive direction with significant enhancement in economy. Moreover, the introduction to omics approach including whole genome sequencing, single cell genomics, proteomics, metagenomics etc., has made it possible to find many unique microbial communities that could be otherwise difficult to cultivate using traditional methods. These findings might be capable enough to state that discovery of extremophiles can bring evolution to biotechnology.

Natural variation in ZmNAC087 contributes to total root length regulation in maize seedlings under salt stress

Soil salinity poses a significant challenge to crop growth and productivity, particularly affecting the root system, which is vital for water and nutrient uptake. To identify genetic factors that influence root elongation in stressful environments, we conducted a genome-wide association study (GWAS) to investigate the natural variation associated with total root length (TRL) under salt stress and normal conditions in maize seedlings. Our study identified 69 genetic variants associated with 38 candidate genes, among which a specific single nucleotide polymorphism (SNP) in ZmNAC087 was significantly associated with TRL under salt stress. Transient expression and transactivation assays revealed that ZmNAC087 encodes a nuclear-localized protein with transactivation activity. Further candidate gene association analysis showed that non-coding variations in ZmNAC087 promoter contribute to differential ZmNAC087 expression among maize inbred lines, potentially influencing the variation in salt-regulated TRL. In addition, through nucleotide diversity analysis, neutrality tests, and coalescent simulation, we demonstrated that ZmNAC087 underwent selection during maize domestication and improvement. These findings highlight the significance of natural variation in ZmNAC087, particularly the favorable allele, in maize salt tolerance, providing theoretical basis and valuable genetic resources for the development of salt-tolerant maize germplasm.

Phyto-microbiome to mitigate abiotic stress in crop plants

Plant-associated microbes include taxonomically diverse communities of bacteria, archaebacteria, fungi, and viruses, which establish integral ecological relationships with the host plant and constitute the phyto-microbiome. The phyto-microbiome not only contributes in normal growth and development of plants but also plays a vital role in the maintenance of plant homeostasis during abiotic stress conditions. Owing to its immense metabolic potential, the phyto-microbiome provides the host plant with the capability to mitigate the abiotic stress through various mechanisms like production of antioxidants, plant growth hormones, bioactive compounds, detoxification of harmful chemicals and toxins, sequestration of reactive oxygen species and other free radicals. A deeper understanding of the structure and functions of the phyto-microbiome and the complex mechanisms of phyto-microbiome mediated abiotic stress mitigation would enable its utilization for abiotic stress alleviation of crop plants and development of stress-resistant crops. This review aims at exploring the potential of phyto-microbiome to alleviate drought, heat, salinity and heavy metal stress in crop plants and finding sustainable solutions to enhance the agricultural productivity. The mechanistic insights into the role of phytomicrobiome in imparting abiotic stress tolerance to plants have been summarized, that would be helpful in the development of novel bioinoculants. The high-throughput modern approaches involving candidate gene identification and target gene modification such as genomics, metagenomics, transcriptomics, metabolomics, and phyto-microbiome based genetic engineering have been discussed in wake of the ever-increasing demand of climate resilient crop plants.

Halobacteria-Based Biofertilizers: A Promising Alternative for Enhancing Soil Fertility and Crop Productivity under Biotic and Abiotic Stresses-A Review

Abiotic and biotic stresses such as salt stress and fungal infections significantly affect plant growth and productivity, leading to reduced crop yield. Traditional methods of managing stress factors, such as developing resistant varieties, chemical fertilizers, and pesticides, have shown limited success in the presence of combined biotic and abiotic stress factors. Halotolerant bacteria found in saline environments have potential as plant promoters under stressful conditions. These microorganisms produce bioactive molecules and plant growth regulators, making them a promising agent for enhancing soil fertility, improving plant resistance to adversities, and increasing crop production. This review highlights the capability of plant-growth-promoting halobacteria (PGPH) to stimulate plant growth in non-saline conditions, strengthen plant tolerance and resistance to biotic and abiotic stressors, and sustain soil fertility. The major attempted points are: (i) the various abiotic and biotic challenges that limit agriculture sustainability and food safety, (ii) the mechanisms employed by PGPH to promote plant tolerance and resistance to both biotic and abiotic stressors, (iii) the important role played by PGPH in the recovery and remediation of agricultural affected soils, and (iv) the concerns and limitations of using PGHB as an innovative approach to boost crop production and food security.

Medicinal plant-associated rhizobacteria enhance the production of pharmaceutically important bioactive compounds under abiotic stress conditions

Interest in cultivating valuable medicinal plants to collect bioactive components has risen extensively over the world to meet the demands of health care systems, pharmaceuticals, and food businesses. Farmers commonly use chemical fertilizers to attain maximal biomass and yield, which have negative effects on the growth, development, and bioactive constituents of such medicinally important plants. Because of its low cost, environmentally friendly behavior, and nondestructive impact on soil fertility, plant health, and human health, the use of beneficial rhizobial microbiota is an alternative strategy for increasing the production of useful medicinal plants under both standard and stressed conditions. Plant growth-promoting rhizobacteria (PGPR) associated with medicinal plants belong to the genera Azotobacter, Acinetobacter, Bacillus, Brevibacterium, Burkholderia, Exiguobacterium, Pseudomonas, Pantoea, Mycobacterium, Methylobacterium, and Serratia. These microbes enhance plant growth parameters by producing secondary metabolites, including enzymes and antibiotics, which help in nutrient uptake, enhance soil fertility, improve plant growth, and protect against plant pathogens. The role of PGPR in the production of biomass and their effect on the quality of bioactive compounds (phytochemicals) is described in this review. Additionally, the mitigation of environmental stresses including drought stress, saline stress, alkaline stress, and flooding stress to herbal plants is illustrated.

Halophytes for the sustainable remediation of heavy metal-contaminated sites: Recent developments and future perspectives

Increasing land degradation by high level of metal wastes is of prime concern for the global research communities. In this respect, halophytes having specific features like salt glands, exclusion of excess ions, heavy metals (HMs) compartmentalization, large pool of antioxidants, and associations with metal-tolerant microbes are of great promise in the sustainable clean-up of contaminated sites. However, sustainable clean-up of HMs by a particular halophyte plant species is governed considerably by physico-chemical characteristics of soil and associated microbial communities. The present review has shed light on the superiority of halophytes over non-halophytes, mechanisms of metal-remediation, recent developments and future perspectives pertaining to the utilization of halophytes in management of HM-contaminated sites with the aid of bibliometric analysis. The results revealed that the research field is receiving considerable attention in the last 5-10 years by publishing ∼50-90% documents with an annual growth rate of 15.41% and citations per document of 29.72. Asian (viz., China, India, and Pakistan) and European (viz., Spain, Portugal, Belgium, Argentina) countries have been emerged as the major regions conducting and publishing extensive research on this topic. The investigations conducted both under in vitro and field conditions have reflected the inherent potential of halophyte as sustainable research tool for successfully restoring the HM-contaminated sites. The findings revealed that the microbial association with halophytes under different challenging conditions is a win-win approach for metal remediation. Therefore, exploration of new halophyte species and associated microorganisms (endophytic and rhizospheric) from different geographical locations, and identification of genes conferring tolerance and phytoremediation of metal contaminants would further advance the intervention of halophytes for sustainable ecological restoration.

Microbial seed coating: An attractive tool for sustainable agriculture

Seed coating is considered one of the best methods to promote sustainable agriculture where the physical and physiological properties of seeds can be improved to facilitate planting, increase growth indices and alleviate abiotic and biotic stresses. Several methods of seed coating are used to attain good application uniformity and adherence in the seed coating process. Seed coating has been tested in seeds of various plant species with different dimensions, forms, textures, and germination types. Plant beneficial microorganisms (PBM), such as rhizobia, bacteria, and fungi inoculated via seed inoculation can increase seed germination, plant performance and tolerance across biotic (e.g., pathogens and pests) and abiotic stress (e.g., salt, drought, and heavy metals) while reducing the use of agrochemical inputs. In this review, the microbial seed coating process and their ability to increase seed performance and protect plants from biotic and abiotic stresses are well discussed and highlighted in sustainable agricultural systems.

Bioinoculants as mitigators of multiple stresses: A ray of hope for agriculture in the darkness of climate change

Plant encounters various biotic and abiotic stresses, that affect agricultural productivity and reduce farmer's income especially under changing global climate. These environmental stresses can advance plant senescence by inducing osmotic stress, nutrient stress, hormonal imbalance, production of oxygen radicals, and ion toxicity, etc. Additionally, these stresses are not limited to plant health but also deteriorate soil health by affecting the microbial diversity of soil. To tackle this global delinquent of agriculture, several methods are suggested to ameliorate the negative effect of different types of stresses, the application of beneficial microorganisms or bioinoculants is one of them. Beneficial microorganisms that are used as bioinoculants not only facilitate plant growth by fulfilling the nutrient requirements but also assist the plant to withstand these stresses. These microorganisms produce certain chemicals such as 1-aminocyclopropane-1-carboxylate (ACC) deaminase, phytohormones, antioxidants, extracellular polysaccharide (EPS), siderophores, antibiotics, and volatile organic compounds (VOCs), etc. which help the plants to mitigate various stresses. Besides, these microbes also activate plant defence responses. Thus, these bioinoculants can effectively replace chemical inputs to supplement nutrient requirements and mitigation of multiple stresses in plants.

Mitigating abiotic stress: microbiome engineering for improving agricultural production and environmental sustainability

The responses of plants to different abiotic stresses and mechanisms involved in their mitigation are discussed. Production of osmoprotectants, antioxidants, enzymes and other metabolites by beneficial microorganisms and their bioengineering ameliorates environmental stresses to improve food production. Progressive intensification of global agriculture, injudicious use of agrochemicals and change in climate conditions have deteriorated soil health, diminished the microbial biodiversity and resulted in environment pollution along with increase in biotic and abiotic stresses. Extreme weather conditions and erratic rains have further imposed additional stress for the growth and development of plants. Dominant abiotic stresses comprise drought, temperature, increased salinity, acidity, metal toxicity and nutrient starvation in soil, which severely limit crop production. For promoting sustainable crop production in environmentally challenging environments, use of beneficial microbes has emerged as a safer and sustainable means for mitigation of abiotic stresses resulting in improved crop productivity. These stress-tolerant microorganisms play an effective role against abiotic stresses by enhancing the antioxidant potential, improving nutrient acquisition, regulating the production of plant hormones, ACC deaminase, siderophore and exopolysaccharides and accumulating osmoprotectants and, thus, stimulating plant biomass and crop yield. In addition, bioengineering of beneficial microorganisms provides an innovative approach to enhance stress tolerance in plants. The use of genetically engineered stress-tolerant microbes as inoculants of crop plants may facilitate their use for enhanced nutrient cycling along with amelioration of abiotic stresses to improve food production for the ever-increasing population. In this chapter, an overview is provided about the current understanding of plant-bacterial interactions that help in alleviating abiotic stress in different crop systems in the face of climate change. This review largely focuses on the importance and need of sustainable and environmentally friendly approaches using beneficial microbes for ameliorating the environmental stresses in our agricultural systems.

Deciphering the genetic and functional diversity of cultivable bacteria from chasmophytic pigweed (Chenopodium album) from Tsomoriri, Ladakh, India

Chasmophytes are a group of diverse plants growing on cracks and crevices of rocks. They survive under nutrient and water-limited conditions. Microorganisms associated with chasmophytes may play a critical role in their survival. In the present study, 263 bacterial isolates were obtained from chasmophytic wild Chenopodium collected from Tsomoriri, Ladakh. Members of Enterobacter, Pseudomonas, Pantoea, and Alcaligenes comprised ~ 90% of the Gram-negative bacteria, while among Gram-positive, Bacillus, Solibacillus, Fictibacillus, Microbacterium, and Micrococcus were most abundant. When evaluated for various plant growth-promoting traits, 36 bacteria could solubilize insoluble phosphate, 10 bacteria could release potassium from silicate minerals, and 25 bacteria could solubilize ZnO, while 124 bacteria produced siderophores. ACC deaminase activity was present in 31 isolates, while 46 bacteria could produce IAA (10.40-232.0 μg/mL). Furthermore, more than 64% of the isolates could grow at 50 °C, while ~ 60% could grow at 4 °C. Similarly, ~ 50% isolates were able to grow with > 1.7 M NaCl and ~ 70% could grow under high osmolarity (~ 67 mOsmol/L). The ability of these microorganisms to grow under such a wide range of temperature, salinity, and osmolarity offers adaptive advantage to colonize plants surviving under harsh environmental conditions. A large number (30-49%) of these isolates could produce acids from various sugars and sugar alcohols which is crucial to release mineral nutrients trapped in the rocks. The results indicated that genetically and functionally diverse microflora associated with wild Chenopodium might be helping these plants to effectively mine nutrients and water under extreme conditions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03278-0.

Overview of biofertilizers in crop production and stress management for sustainable agriculture

With the increase in world population, the demography of humans is estimated to be exceeded and it has become a major challenge to provide an adequate amount of food, feed, and agricultural products majorly in developing countries. The use of chemical fertilizers causes the plant to grow efficiently and rapidly to meet the food demand. The drawbacks of using a higher quantity of chemical or synthetic fertilizers are environmental pollution, persistent changes in the soil ecology, physiochemical composition, decreasing agricultural productivity and cause several health hazards. Climatic factors are responsible for enhancing abiotic stress on crops, resulting in reduced agricultural productivity. There are various types of abiotic and biotic stress factors like soil salinity, drought, wind, improper temperature, heavy metals, waterlogging, and different weeds and phytopathogens like bacteria, viruses, fungi, and nematodes which attack plants, reducing crop productivity and quality. There is a shift toward the use of biofertilizers due to all these facts, which provide nutrition through natural processes like zinc, potassium and phosphorus solubilization, nitrogen fixation, production of hormones, siderophore, various hydrolytic enzymes and protect the plant from different plant pathogens and stress conditions. They provide the nutrition in adequate amount that is sufficient for healthy crop development to fulfill the demand of the increasing population worldwide, eco-friendly and economically convenient. This review will focus on biofertilizers and their mechanisms of action, role in crop productivity and in biotic/abiotic stress tolerance.

Microbial Diversity and Adaptation under Salt-Affected Soils: A Review

The salinization of soil is responsible for the reduction in the growth and development of plants. As the global population increases day by day, there is a decrease in the cultivation of farmland due to the salinization of soil, which threatens food security. Salt-affected soils occur all over the world, especially in arid and semi-arid regions. The total area of global salt-affected soil is 1 billion ha, and in India, an area of nearly 6.74 million ha−1 is salt-stressed, out of which 2.95 million ha−1 are saline soil (including coastal) and 3.78 million ha−1 are alkali soil. The rectification and management of salt-stressed soils require specific approaches for sustainable crop production. Remediating salt-affected soil by chemical, physical and biological methods with available resources is recommended for agricultural purposes. Bioremediation is an eco-friendly approach compared to chemical and physical methods. The role of microorganisms has been documented by many workers for the bioremediation of such problematic soils. Halophilic Bacteria, Arbuscular mycorrhizal fungi, Cyanobacteria, plant growth-promoting rhizobacteria and microbial inoculation have been found to be effective for plant growth promotion under salt-stress conditions. The microbial mediated approaches can be adopted for the mitigation of salt-affected soil and help increase crop productivity. A microbial product consisting of beneficial halophiles maintains and enhances the soil health and the yield of the crop in salt-affected soil. This review will focus on the remediation of salt-affected soil by using microorganisms and their mechanisms in the soil and interaction with the plants.

Characterization of Siccibacter sp. Strain C2 a Novel Rhizobacterium that Enhances Tolerance of Barley to Salt Stress

Plant growth promoting rhizobacteria (PGPR) arouse an increasing interest as an eco-friendly solution for improving crop tolerance to environmental stresses. In this study, we report the characterization of a novel halotolerant PGPR strain (named C2) identified in a screen of rhizospheric bacterial isolates from southeast of Tunisia. Phylogenetic analysis showed that strain C2 is most likely affiliated to the genus Siccibacter with Siccibacter turicensis as the closest species (98.19%). This strain was able to perform phosphate solubilization and production of indole acetic acid (IAA), siderophores, hydrogen cyanide (HCN), as well as different hydrolytic enzymes (proteases, amylases, cellulases, and lipases). The potential of strain C2 in enhancing salt stress tolerance of Hordeum vulgare was also investigated. Our greenhouse inoculation assays showed that strain C2 promotes barley growth in the presence of 400 mM NaCl by increasing biomass, root length, and chlorophyll contents. It has a positive effect on the photosynthetic efficiency, concomitantly with lower intercellular CO₂ contents, compared to non-inoculated plants. Moreover, barley inoculation with strain C2 under salt stress, resulted in higher accumulation of proline and soluble sugars and alleviate the oxidative stress by decreasing hydrogen peroxide and malondialdehyde contents. Remarkably, this positive effect corroborates with a significant activation in the expression of a subset of barley stress responsive genes, including HVA1, HvDREB1, HvWRKY38 and HvP5CS. In summary, Siccibacter sp. strain C2 is able to enhance barley salt stress tolerance and should be leveraged in developing sustainable practices for cereal crop production.

What Did We Learn From Current Progress in Heat Stress Tolerance in Plants? Can Microbes Be a Solution?

Temperature is a significant parameter in agriculture since it controls seed germination and plant growth. Global warming has resulted in an irregular rise in temperature posing a serious threat to the agricultural production around the world. A slight increase in temperature acts as stress and exert an overall negative impact on different developmental stages including plant phenology, development, cellular activities, gene expression, anatomical features, the functional and structural orientation of leaves, twigs, roots, and shoots. These impacts ultimately decrease the biomass, affect reproductive process, decrease flowering and fruiting and significant yield losses. Plants have inherent mechanisms to cope with different stressors including heat which may vary depending upon the type of plant species, duration and degree of the heat stress. Plants initially adapt avoidance and then tolerance strategies to combat heat stress. The tolerance pathway involves ion transporter, osmoprotectants, antioxidants, heat shock protein which help the plants to survive under heat stress. To develop heat-tolerant plants using above-mentioned strategies requires a lot of time, expertise, and resources. On contrary, plant growth-promoting rhizobacteria (PGPRs) is a cost-effective, time-saving, and user-friendly approach to support and enhance agricultural production under a range of environmental conditions including stresses. PGPR produce and regulate various phytohormones, enzymes, and metabolites that help plant to maintain growth under heat stress. They form biofilm, decrease abscisic acid, stimulate root development, enhance heat shock proteins, deamination of ACC enzyme, and nutrient availability especially nitrogen and phosphorous. Despite extensive work done on plant heat stress tolerance in general, very few comprehensive reviews are available on the subject especially the role of microbes for plant heat tolerance. This article reviews the current studies on the retaliation, adaptation, and tolerance to heat stress at the cellular, organellar, and whole plant levels, explains different approaches, and sheds light on how microbes can help to induce heat stress tolerance in plants.

Soil Microbes Drive the Flourishing Growth of Plants From Leucocalocybe mongolica Fairy Ring

Fairy ring is a natural phenomenon in which fungal fruiting bodies occur as a ring on a spot. This ring is produced due to spore ejection by Basidiomycetous fungi and forms a lush growing plant belt. However, the drivers for such formations and the potential plant growth-promoting rhizobacteria in fairy ring soils remain unknown. Fairy rings formed by Leucocalocybe mongolica were selected in this study. Soil characteristics and microbial (bacteria and fungi) community structures between beneath and outside the fairy rings were compared through high-throughput sequencing. Beneficial bacterial resources were excavated using dependent culturable methods. Soil electrical conductivity and available potassium were higher in the soil beneath the ring than outside it. These parameters were positively correlated with the dominant microbial community, but microbial diversity was lower. In the soil beneath the fairy ring, Bacteroidetes and Basidiomycota were more abundant, whereas Verrucomicrobia was less prevalent. Bacillus pumilus (strain BG-5) was isolated from the soil beneath the ring. Strain BG-5 can solubilize phosphorus and produce indole-3-acetic acid, NH4 +, and siderophores. Furthermore, strain BG-5 enhanced salt tolerance and promoted the growth of Arabidopsis thaliana, wheat (Triticum aestivum), and cotton (Gossypium hirsutum) seedlings. This study indicated the presence of abundant beneficial microbes driving the flourishing growth of plants in the fairy ring soil and provided bio-resources for agricultural growth-promoting agents.

Plant growth promoting characteristics of halophilic and halotolerant bacteria isolated from coastal regions of Saurashtra Gujarat

Halophiles are a class of microorganisms that thrive in environments with very high salt concentrations. The coastal regions of Saurashtra Gujarat host a diverse group of microorganisms including halophilic and halotolerant bacteria that may have plant growth promoting characteristics. Microorganisms with plant growth promoting characteristics are of immense importance in the field of agriculture and the present study was conducted to investigate the characteristics of halophilic and halotolerant bacteria isolated from agricultural soils of coastal regions of Junagadh and Porbandar districts of Saurashtra, Gujarat. A total of 15 isolated strains showed indole acetic acid production, solubilization of phosphate and potash, and nitrogen fixing capacity ranging from 18.77-33.48 μg ml^-1, 50.10-106.10%, 180.42-239.92% and 0.170-0.480 g kg^-1 of Jensen's agar medium, respectively, while two isolates were also found positive for siderophore production. Besides, nine out of fifteen isolates also showed positive ACC deaminase activity ranging from 0.92-5.78 µM α-ketobutyrate mg^-1 h^-1. The isolates were further characterized by physiological, microscopic, and biochemical tests. The halophilic and halotolerant bacterial isolates were identified by 16S rRNA gene sequencing as belonging to Halomonas pacifica, H. stenophila, and Bacillus haynesii, B. licheniformis and Oceanobacillus aidingensis respectively. The 16S rRNA partial gene sequence of two isolates belonging to H. pacifica and H. stenophila were submitted to NCBI with accession number MK955347 and MK961217 respectively. The findings of the present investigation showed that isolated bacterial halophiles possess promising plant growth promoting characteristics. Their potential as bioinoculants to alleviate salinity stress in crops and for bioremediation deserves further investigation.

Taxonomic and Functional Diversity of Rhizosphere Microbiome Recruited From Compost Synergistically Determined by Plant Species and Compost

Compost is frequently served as the first reservoir for plants to recruit rhizosphere microbiome when used as growing substrate in the seedling nursery. In the present study, recruitment of rhizosphere microbiome from two composts by tomato, pepper, or maize was addressed by shotgun metagenomics and 16S rRNA amplicon sequencing. The 16S rRNA amplicon sequencing analysis showed that 41% of variation in the rhizosphere bacterial community was explained by compost, in contrast to 23% by plant species. Proteobacterial genera were commonly recruited by all three plant species with specific selections for Ralstonia by tomato and Enterobacteria by maize. These findings were confirmed by analysis of 16S rRNA retrieved from the shotgun metagenomics library. Approximately 70% of functional gene clusters differed more than sevenfold in abundance between rhizosphere and compost. Functional groups associated with the sensing and up-taking of C3 and C4 carboxylic acids, amino acids, monosaccharide, production of antimicrobial substances, and antibiotic resistance were over-represented in the rhizosphere. In summary, compost and plant species synergistically shaped the composition of the rhizosphere microbiome and selected for functional traits associated with the competition on root exudates.

Teamwork to Survive in Hostile Soils: Use of Plant Growth-Promoting Bacteria to Ameliorate Soil Salinity Stress in Crops

Plants and their microbiomes, including plant growth-promoting bacteria (PGPB), can work as a team to reduce the adverse effects of different types of stress, including drought, heat, cold, and heavy metals stresses, as well as salinity in soils. These abiotic stresses are reviewed here, with an emphasis on salinity and its negative consequences on crops, due to their wide presence in cultivable soils around the world. Likewise, the factors that stimulate the salinity of soils and their impact on microbial diversity and plant physiology were also analyzed. In addition, the saline soils that exist in Mexico were analyzed as a case study. We also made some proposals for a more extensive use of bacterial bioinoculants in agriculture, particularly in developing countries. Finally, PGPB are highly relevant and extremely helpful in counteracting the toxic effects of soil salinity and improving crop growth and production; therefore, their use should be intensively promoted.

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.

Understanding the potential of root microbiome influencing salt-tolerance in plants and mechanisms involved at the transcriptional and translational level

Soil salinity severely affects plant growth and development and imparts inevitable losses to crop productivity. Increasing the concentration of salts in the vicinity of plant roots has severe consequences at the morphological, biochemical, and molecular levels. These include loss of chlorophyll, decrease in photosynthetic rate, reduction in cell division, ROS generation, inactivation of antioxidative enzymes, alterations in phytohormone biosynthesis and signaling, and so forth. The association of microorganisms, viz. plant growth-promoting rhizobacteria, endophytes, and mycorrhiza, with plant roots constituting the root microbiome can confer a greater degree of salinity tolerance in addition to their inherent ability to promote growth and induce defense mechanisms. The mechanisms involved in induced stress tolerance bestowed by these microorganisms involve the modulation of phytohormone biosynthesis and signaling pathways (including indole acetic acid, gibberellic acid, brassinosteroids, abscisic acid, and jasmonic acid), accumulation of osmoprotectants (proline, glycine betaine, and sugar alcohols), and regulation of ion transporters (SOS1, NHX, HKT1). Apart from this, salt-tolerant microorganisms are known to induce the expression of salt-responsive genes via the action of several transcription factors, as well as by posttranscriptional and posttranslational modifications. Moreover, the potential of these salt-tolerant microflora can be employed for sustainably improving crop performance in saline environments. Therefore, this review will briefly focus on the key responses of plants under salinity stress and elucidate the mechanisms employed by the salt-tolerant microorganisms in improving plant tolerance under saline environments.

Antimicrobial activity of bacteria associated with the rhizosphere and phyllosphere of Avena fatua and Brachiaria reptans

Environmental pollution especially heavy metal-contaminated soils adversely affects the microbial communities associated with the rhizosphere and phyllosphere of plants growing in these areas. In the current study, we identified and characterized the rhizospheric and phyllospheric bacterial strains from Avena fatua and Brachiaria reptans with the potential for antimicrobial activity and heavy metal resistance. A total of 18 bacterial strains from the rhizosphere and phyllosphere of A. fatua and 19 bacterial strains from the rhizosphere and phyllosphere of B. reptans were identified based on 16S rRNA sequence analysis. Bacterial genera, including Bacillus, Staphylococcus, Pseudomonas, and Enterobacter were dominant in the rhizosphere and phyllosphere of A. fatua and Bacillus, Marinobacter, Pseudomonas, Enterobacter, and Kocuria, were the dominating bacterial genera from the rhizosphere and phyllosphere of B. reptans. Most of the bacterial strains were resistant to heavy metals (Cd, Pb, and Cr) and showed antimicrobial activity against different pathogenic bacterial strains. The whole-genome sequence analysis of Pseudomonas putida BR-PH17, a strain isolated from the phyllosphere of B. reptans, was performed by using the Illumina sequencing approach. The BR-PH17 genome contained a chromosome with a size of 5774330 bp and a plasmid DNA with 80360 bp. In this genome, about 5368 predicted protein-coding sequences with 5539 total genes, 22 rRNAs, and 75 tRNA genes were identified. Functional analysis of chromosomal and plasmid DNA revealed a variety of enzymes and proteins involved in antibiotic resistance and biodegradation of complex organic pollutants. These results indicated that bacterial strains identified in this study could be utilized for bioremediation of heavy metal-contaminated soils and as a novel source of antimicrobial drugs.

Whole genome analysis of Gluconacetobacter azotocaptans DS1 and its beneficial effects on plant growth

Plant-associated bacteria play an important role in the enhancement of plant growth and productivity. Gluconacetobacter azotocaptans is an exceptional bacterium considering that till today it has been isolated and reported only from Mexico and Canada. It is a plant growth-promoting bacterium and can be used as biofertilizer for different crops and vegetables. The objective of the current study was to evaluate the inoculation effect of Gluconacetobacter azotocaptans DS1, Pseudomonas putida CQ179, Azosprillium zeae N7, Azosprillium brasilense N8, and Azosprillium canadense DS2, on the growth of vegetables including cucumber, sweet pepper, radish, and tomato. All strains increased the vegetables' growth; however, G. azotocaptans DS1 showed better results as compared to other inoculated and control plants and significantly increased the plant biomass of all vegetables. Therefore, the whole genome sequence of G. azotocaptans DS1 was analyzed to predict genes involved in plant growth promotion, secondary metabolism, antibiotics resistance, and bioremediation of heavy metals. Results of genome analysis revealed that G. azotocaptans DS1 has a circular chromosome with a size of 4.3 Mbp and total 3898 protein-coding sequences. Based on functional analysis, genes for nitrogen fixation, phosphate solubilization, indole acetic acid, phenazine, siderophore production, antibiotic resistance, and bioremediation of heavy metals including copper, zinc, cobalt, and cadmium were identified. Collectively, our findings indicated that G. azotocaptans DS1 can be used as a biofertilizer and biocontrol agent for growth enhancement of different crops and vegetables.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02996-1.

Comparative Study of the Rhizosphere and Root Endosphere Microbiomes of Cholistan Desert Plants

Microbial communities associated with the rhizosphere and roots of desert halophytes play an important role in plants’ growth and development. Very limited information has been available on the microbial diversity of arid environments of Pakistan. Hence in the current study, the microbial diversity of rhizosphere and root endosphere of desert halophytes, Zygophyllum simplex, Haloxylon salicoricum, Aerva javanica, and Capparis decidua was evaluated. The rhizosphere and root endosphere samples of desert halophytes collected from the three geographic sites of Cholistan desert, Punjab, Pakistan were analyzed by using 16S rRNA based Illumina sequencing. The results showed that Proteobacteria were more abundant in the rhizospheric soils while Actinobacteria were more dominant in the root endosphere of halophytes. Bacteroidetes, Firmicutes, and Deinococcus-Thermus were identified from all rhizospheric soils and roots across the three sites, with variable percentage. Bacillus, Kocuria, Pseudomonas, Halomonas, and Flavobacterium were commonly identified from the rhizosphere and root endosphere of halophytes across all the three sites. At the genus level, microbial diversity from Haloxylon showed the greatest variations between the rhizosphere and root endosphere from the site 2. This study revealed that microbial diversity analysis can be used to study how changes in abiotic factors such as soil moisture content and salinity affect the microbial communities associated with the rhizospheric soils and root endosphere of halophytes across the three sites. This study will also help in the discovery of potential inoculants for crops growing in arid and semi-arid regions of Pakistan.

Secondary Metabolites From Halotolerant Plant Growth Promoting Rhizobacteria for Ameliorating Salinity Stress in Plants

Soil salinization has emerged as one of the prime environmental constraints endangering soil quality and agricultural productivity. Anthropogenic activities coupled with rapid pace of climate change are the key drivers of soil salinity resulting in degradation of agricultural lands. Increasing levels of salt not only impair structure of soil and its microbial activity but also restrict plant growth by causing harmful imbalance and metabolic disorders. Potential of secondary metabolites synthesized by halotolerant plant growth promoting rhizobacteria (HT-PGPR) in the management of salinity stress in crops is gaining importance. A wide array of secondary metabolites such as osmoprotectants/compatible solutes, exopolysaccharides (EPS) and volatile organic compounds (VOCs) from HT-PGPR have been reported to play crucial roles in ameliorating salinity stress in plants and their symbiotic partners. In addition, HT-PGPR and their metabolites also help in prompt buffering of the salt stress and act as biological engineers enhancing the quality and productivity of saline soils. The review documents prominent secondary metabolites from HT-PGPR and their role in modulating responses of plants to salinity stress. The review also highlights the mechanisms involved in the production of secondary metabolites by HT-PGPR in saline conditions. Utilizing the HT-PGPR and their secondary metabolites for the development of novel bioinoculants for the management of saline agro-ecosystems can be an important strategy in the future.

Plant-Growth-Promoting Bacteria Mitigating Soil Salinity Stress in Plants

Soil deterioration has led to problems with the nutrition of the world’s population. As one of the most serious stressors, soil salinization has a negative effect on the quantity and quality of agricultural production, drawing attention to the need for environmentally friendly technologies to overcome the adverse effects. The use of plant-growth-promoting bacteria (PGPB) can be a key factor in reducing salinity stress in plants as they are already introduced in practice. Plants having halotolerant PGPB in their root surroundings improve in diverse morphological, physiological, and biochemical aspects due to their multiple plant-growth-promoting traits. These beneficial effects are related to the excretion of bacterial phytohormones and modulation of their expression, improvement of the availability of soil nutrients, and the release of organic compounds that modify plant rhizosphere and function as signaling molecules, thus contributing to the plant’s salinity tolerance. This review aims to elucidate mechanisms by which PGPB are able to increase plant tolerance under soil salinity.

Bioprospecting of a Novel Plant Growth-Promoting Bacterium Bacillus Altitudinis KP-14 for Enhancing Miscanthus × giganteus Growth in Metals Contaminated Soil

Simple Summary

Marginal land represents poor soil with low agricultural characteristics and crop productivity, which is sometimes additionally contaminated. The exploitation of marginal land for normal agriculture is not possible but it suitable for cultivation of energy crops, especially Miscanthus × giganteus (Mxg), however, the harvest biomass value in such land is lower. The produced Mxg biomass can be converted to alternative energy like biofuel and biogas, or used for production of other value-added products like insulation fibers, building materials or paper, etc. It is well known fact that plant growth-promoting bacteria are beneficial for stimulating the overall development of plants even under stress conditions. In the current study, a number of strains were isolated from the metal-contaminated post-mining land, identified, biochemically characterized, and evaluated for abiotic stress tolerance: pH, temperature, salinity, and heavy metal (lead). Among different isolates, the multiple abiotic stress-tolerant plant growth-promoting bacteria Bacillus altitudinis KP-14 showed the best properties. Its effect on the growth of Mxg under the severe stress of metal-contaminated soil was evaluated. It was found that selected bacterial strain KP-14 significantly enhanced the biomass production. The overall results suggested that B. altitudinis KP-14 can be recommended as a potent biofertilizer for marginal lands.

Abstract

Use of plant growth-promoting bacteria (PGPB) for cultivation of the biofuel crop Miscanthus × giganteus (Mxg) in post-military and post-mining sites is a promising approach for the bioremediation of soils contaminated by metals. In the present study, PGPB were isolated from contaminated soil and screened for tolerance against abiotic stresses caused by salinity, pH, temperature, and lead (Pb). Selected strains were further assessed and screened for plant growth-promoting attributes. The isolate showing the most potential, Bacillus altitudinis KP-14, was tested for enhancement of Mxg growth in contaminated soil under greenhouse conditions. It was found to be highly tolerant to diverse abiotic stresses, exhibiting tolerance to salinity (0–15%), pH (4–8), temperature (4–50 °C), and Pb (up to 1200 ppm). The association of B. altitudinis KP-14 with Mxg resulted in a significant (p ≤ 0.001) impact on biomass enhancement: the total shoot and dry root weights were significantly enhanced by 77.7% and 55.5%, respectively. The significant enhancement of Mxg biomass parameters by application of B. altitudinis KP-14 strongly supports the use of this strain as a biofertilizer for the improvement of plant growth in metal-contaminated soils.

Current perspectives and applications in plant probiotics

As agriculture and food security face unprecedented challenges, emerging agricultural innovations and existing practices require ongoing examination in the context of sustainability. In this review, we focus on the use of probiotic microorganisms for improved plant production. As plants are enormously diverse, emphasis is placed on the fundamental sites of plant-microbe interactions regarding benefits and challenges encountered when altering the microbiome of these locations. The soil, the external plant epidermis, and internal plant tissue are considered in discussion regarding the type of plant probiotic application. Plant probiotics range from broader soil beneficial microorganisms (such as Trichoderma spp.) through to specialised epiphytes and endophytes (such as root nodule bacteria). As each site of interaction affects plant growth differently, potential outcomes from the introduction of these exogenous microorganisms are discussed with regard to plant productivity. Finally, recommendations regarding regulation and future use of plant probiotics are points of consideration throughout this review.