Isolation and characterization of drought resistance bacteria for plant growth promoting properties and their effect on chilli ( Capsicum annuum ) seedling under salt stress

Assessment of Plant Growth-Promoting Parameters of Endophytes Isolated from Calotropis procera and Their Performance Under Irrigated and Non-irrigated Conditions

In the present study, bacterial and fungal endophytes are isolated from Calotropis procera, a drought-resistant plant and studied for their role in plant growth promotion. Among bacterial sp. Enterobacter cloacae subsp. cloacae strain CPR5B and fungus, Penicillium citrinum strain CPL1F, were identified as potent endophytes as both strains were able to produce Indole Acetic Acid (IAA) and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and solubilize phosphate. Penicillium citrinum CPL1F also been shown to produce siderophore. The IAA production was observed to be 94.28 μg/mL and 17.1 μg/mL for bacterial and fungal sp., respectively. The phosphate solubilization was observed to be 76.41 μg/mL and 114.57 μg/mL, respectively. The in vitro plant treatment studies with bacterium and fungus under irrigated and non-irrigated conditions showed that both strains had promoted plant growth in both conditions with respect to their control. Both the strains showed significant changes in most of the growth parameters under endophyte-treated irrigated and non-irrigated conditions, suggesting their stress-dependent plant growth promotion. The present findings will contribute to exploring endophytes that enhance plant growth in adverse conditions and act as plant growth-promoting endophytes.

Pan-metagenome reveals the abiotic stress resistome of cigar tobacco phyllosphere microbiome

The important role of microbial associations in mediating plant protection and responses to abiotic stresses has been widely recognized. However, there have been limited studies on the functional profile of the phyllosphere microbiota from tobacco (Nicotiana tabacum), hindering our understanding of the mechanisms underlying stress resilience in this representative and easy-to-cultivate model species from the solanaceous family. To address this knowledge gap, our study employed shotgun metagenomic sequencing for the first time to analyze the genetic catalog and identify putative plant growth promoting bacteria (PGPB) candidates that confer abiotic stress resilience throughout the growth period of cigar tobacco in the phyllosphere. We identified abundant genes from specific bacterial lineages, particularly Pseudomonas, within the cigar tobacco phyllospheric microbiome. These genes were found to confer resilience against a wide range of stressors, including osmotic and drought stress, heavy metal toxicity, temperature perturbation, organic pollutants, oxidative stress, and UV light damage. In addition, we conducted a virome mining analysis on the metagenome to explore the potential roles of viruses in driving microbial adaptation to environmental stresses. Our results identified a total of 3,320 scaffolds predicted to be viral from the cigar tobacco phyllosphere metagenome, with various phages infecting Pseudomonas, Burkholderia, Enterobacteria, Ralstonia, and related viruses. Within the virome, we also annotated genes associated with abiotic stress resilience, such as alkaline phosphatase D (phoD) for nutrient solubilization and glutamate-5-semialdehyde dehydrogenase (proA) for osmolyte synthesis. These findings shed light on the unexplored roles of viruses in facilitating and transferring abiotic stress resilience in the phyllospheric microbiome through beneficial interactions with their hosts. The findings from this study have important implications for agricultural practices, as they offer potential strategies for harnessing the capabilities of the phyllosphere microbiome to enhance stress tolerance in crop plants.

Biochemical, Catabolic, and PGP Activity of Microbial Communities and Bacterial Strains from the Root Zone of Baccharis linearis in a Mediterranean Mine Tailing

The management of mine tailings (MT) is commonly workload heavy, intrusive, and expensive. Phytostabilization offers a promising approach for MT management; however, it poses challenges due to the unfavorable physicochemical properties of these wastes. Nevertheless, native microorganisms capable of supporting plant growth and development could enhance the efficacy of phytostabilization. This study assesses the biological activity of microbial communities from the root zone of Baccharis linearis, which is naturally present in MT, in order to evaluate their biotechnological potential for phytostabilization. The root zone and bulk samples were collected from B. linearis plants located within a MT in the Mediterranean zone of Chile. Enzyme activities related to the cycling of C, N, and P were assessed. The community-level physiological profile was evaluated using the MicroRespTM system. Bacterial plant growth-promoting (PGP) traits and colony forming units (CFU) were evaluated through qualitative and microbiological methods, respectively. CFU, enzyme activities, and CLPP were higher in the root zone compared with the bulk samples. Five bacterial strains from the root zone exhibited PGP traits such as P solubilization and N acquisition, among others. The presence of microbial communities in the root zone of B. linearis with PGP traits suggests their potential to enhance the ecological management of MT through phytostabilization programs.

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

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

Screening of osmotic stress-tolerant bacteria for plant growth promotion in wheat (Triticum aestivum L.) and brinjal (Solanum melongena L.) under drought conditions

Drought stress adversely affects plant growth and productivity. Therefore, the application of plant growth-promoting bacteria (PGPB) is a viable option for combating drought resistance in crops. In this study, 144 bacteria were isolated from the Kutch desert soil in Gujarat. Based on osmotic stress tolerance and PGP properties, two strains, Bacillus tequilensis (KS5B) and Pseudomonas stutzeri (KS5C) were tested for their effect on wheat (Triticum aestivum L.) and brinjal (Solanum melongena L.) under drought stress conditions. Inoculation with osmotic stress-tolerant bacteria showed 15.15-29.27% enhancement in root length of wheat and 15.27-32.59% in brinjal plants. Similarly, the enhancement of shoot length ranged from 14.72-37.70% for wheat and 59.39-95.94% for brinjal plants. Furthermore, the inoculated plants showed significant improvement in chlorophyll content and antioxidant properties such as proline, peroxidase, and polyphenol oxidase activity compared the control. Therefore, the bacterial strains identified in this study can be used to mitigate drought stress and enhance plant biomass.

Harnessing rhizobacteria to fulfil inter-linked nutrient dependency on soil and alleviate stresses in plants

Plant rhizo-microbiome comprises of complex microbial communities that colonizes at the interphase of plant roots and soil. Plant-growth-promoting rhizobacteria (PGPR) in the rhizosphere provides important ecosystem services ranging from release of essential nutrients for enhancing soil quality and improving plant health to imparting protection to plants against rising biotic and abiotic stresses. Hence, PGPR serve as restoring agents to rejuvenate soil health and mediate plant fitness in the facet of changing climate. Though, it is evident that nutrients availability in soil are managed through inter-linked mechanisms, how PGPR expediate these processes remain less recognized. Promising results of PGPR inoculation on plant growth are continually reported in controlled environmental conditions, however, their field application often fails due to competition with native microbiota and low colonization efficiency in roots. The development of highly efficient and smart bacterial synthetic communities by integrating bacterial ecological and genetic features provides better opportunities for successful inoculant formulations. This review provides an overview of the inter-play between nutrient availability and disease suppression governed by rhizobacteria in soil followed by the role of synthetic bacterial communities in developing efficient microbial inoculants. Moreover, an outlook on the beneficial activities of rhizobacteria in modifying soil characteristics to sustainably boost agroecosystem functioning is also provided.

Graphene oxide influence in soil bacteria is dose dependent and changes at osmotic stress: growth variation, oxidative damage, antioxidant response, and plant growth promotion traits of a Rhizobium strain

Climate change events, such as drought, are increasing and soil bacteria can be severely affected. Moreover, the accumulation of emerging pollutants is expected to rapidly increase, and their impact on soil organisms, their interactions, and the services they provide is poorly known. The use of graphene oxide (GO) has been increasing due to its enormous potential for application in several areas and it is expected that concentration in soil will increase in the future, potentially causing disturbances in soil microorganisms not yet identified.Here we show the effects that GO nanosheets can cause on soil bacteria, in particular those that promote plant growth, in control and 10% polyethylene glycol (PEG) conditions. Low concentrations of GO nanosheets did not affect the growth of Rhizobium strain E20-8, but under osmotic stress (PEG) GO decreased bacterial growth even at lower concentrations. GO caused oxidative stress, with antioxidant mechanisms being induced to restrain damage, effectively at lower concentrations, but less effective at higher concentrations, and oxidative damage overcame. Under osmotic stress, alginate and glycine betaine osmoregulated the bacteria. Simultaneous exposure to PEG and GO induced oxidative damage. Plant growth promotion traits (indole acetic acid and siderophores production) were increased by osmotic stress and GO did not disturb these abilities. In the context of climate change, our findings might be relevant as they can form the premises for the implementation of crop production methodologies adapted to the new prevailing conditions, which include the presence of nanoparticles in the soil and more frequent and severe drought.

Molecular characterization of endophytic and ectophytic plant growth promoting bacteria isolated from tomato plants (Solanum lycopersicum L.) grown in different soil types

Background

Successful rhizosphere colonization by plant growth promoting rhizobacteria (PGPR) is of crucial importance to perform the desired plant growth promoting activities. Since rhizocompetence is a dynamic process influenced by surrounding environmental conditions. In the present study, we hypothesized that bacterial isolates obtained from different tomato plant microhabitats (balk soil, rhizosphere, endorhiza, phyllosphere, and endoshoot) grown in different soils (sand, clay, and peat moss) will show different rhizocompetence abilities.

Results

To evaluate this hypothesis, bacterial isolates were obtained from different plant microhabitats and screened for their phosphate solubilizing and nitrogen fixing activates. BOX-PCR fingerprint profiles showed high genotypic diversity among the tested isolates and that same genotypes were shared between different soils and/or plant microhabitats. 16S rRNA gene sequences of 25 PGP isolates, representing different plant spheres and soil types, were affiliated to eight genera: Enterobacter, Paraburkholderia, Klebsiella, Bacillus, Paenibacillus, Stenotrophomonas, Pseudomonas, and Kosakonia. The rhizocompetence of each isolate was evaluated in the rhizosphere of tomato plants grown on a mixture of the three soils. Different genotypes of the same bacterial species displayed different rhizocompetence potentials. However, isolates obtained from the above-ground parts of the plant showed high rhizocompetence. In addition, biological control-related genes, ituD and srfC, were detected in the obtained spore forming bacterial isolates.

Conclusion

This study evaluates, for the first time, the relationship between plant microhabitat and the rhizocompetence ability in tomato rhizosphere. The results indicated that soil type and plant sphere can influence both the genotypic diversity and rhizocompetence ability of the same bacterial species. Bacterial isolates obtained in this study are promising to be used as an environmentally friendly substitution of chemical fertilizers.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-022-00361-0.

Predatory activity of Acanthamoeba sp genotype T4 on different plant growth-promoting bacteria and their combined effect on rice seedling growth

Heterotrophic protists play a crucial role in plant growth promotion via nutrient cycling and shift in microbial community composition in the soil ecosystem. Selective predation pressure by protists contributes to the evaluation of plant beneficial traits in rhizospheric bacteria. However, not always all plant growth-promoting bacterial (PGPB) strains are benefitted by predation. This study aimed to examine the predatory effect of Acanthamoeba sp genotype T4 on a range of PGPB strains and their combined impact on early rice seedling growth. Acanthamoeba sp isolated from rice rhizosphere soils were used to assess predation against several PGPB such as Pseudomonas, Bacillus, Enterobacter, Morganella, Stenotrophomonas, Providencia, and Lysinibacillus on Nutrient Yeast Extract agar (NYE) plate. The controlled experiment on the germinated rice seeds (Oryza sativa L.) grown in Petri dishes containing each PGPB strain and Acanthamoeba sp was performed to evaluate the combined impact on plant performance. The PGPB-Acanthamoeba combined treatments in Petri dishes showed significant rice seedling growth compared to PGPB alone, non-PGPB and control. Our results indicated the positive but different impact of Acanthamoeba sp with different PGPB species on early rice plant growth. Further in-depth research should be carried out with diverse protists and PGPB species to assess which protist species can be linked to enhancement of indigenous soil PGPB for improved plant growth.

Plant Responses to Abiotic Stresses and Rhizobacterial Biostimulants: Metabolomics and Epigenetics Perspectives

In response to abiotic stresses, plants mount comprehensive stress-specific responses which mediate signal transduction cascades, transcription of relevant responsive genes and the accumulation of numerous different stress-specific transcripts and metabolites, as well as coordinated stress-specific biochemical and physiological readjustments. These natural mechanisms employed by plants are however not always sufficient to ensure plant survival under abiotic stress conditions. Biostimulants such as plant growth-promoting rhizobacteria (PGPR) formulation are emerging as novel strategies for improving crop quality, yield and resilience against adverse environmental conditions. However, to successfully formulate these microbial-based biostimulants and design efficient application programs, the understanding of molecular and physiological mechanisms that govern biostimulant-plant interactions is imperatively required. Systems biology approaches, such as metabolomics, can unravel insights on the complex network of plant-PGPR interactions allowing for the identification of molecular targets responsible for improved growth and crop quality. Thus, this review highlights the current models on plant defence responses to abiotic stresses, from perception to the activation of cellular and molecular events. It further highlights the current knowledge on the application of microbial biostimulants and the use of epigenetics and metabolomics approaches to elucidate mechanisms of action of microbial biostimulants.

Potential of plant beneficial bacteria and arbuscular mycorrhizal fungi in phytoremediation of metal-contaminated saline soils

Phytoremediation has been considered as a promising technique to decontaminate polluted soils. However, climatic stress particularly salinity, is a potential threat to soil properties and plant growth, thus restricting the employment of this technology. The aim of this study was to access the impact of microbial inoculation on phytoremediation of nickel (Ni) contaminated saline soils using Helianthus annuus. Salt resistant plant beneficial bacterium (PBB) Pseudomonas libanensis TR1 and arbuscular mycorrhizal fungus (AMF) Claroideoglomus claroideum BEG210 were used. Inoculation of P. libanensis alone or in combination with C. claroideum significantly enhanced plant growth, changed physiological status (e.g. electrolyte leakage, chlorophyll, proline and malondialdehyde contents) as well as Ni and sodium (Na⁺) accumulation potential (e.g. uptake and translocation factor of Ni and Na⁺) of H. annuus under Ni and salinity stress either alone or in combination. These results revealed that bioaugmentation of microbial strains may serve as a preferred strategy for improving phytoremediation of metal-polluted saline soils.

Phytoextraction of iron from contaminated soils by inoculation of iron-tolerant plant growth-promoting bacteria in Brassica juncea L. Czern

Iron (Fe) is one of the essential micronutrients for all living organisms. Despite its abundance in most of the contaminated soil, it is usually in unavailable forms. The unavailable form of Fe could be mobilized to plants by the use of microorganisms. This study was carried out to show that the Fe-contaminated field soils could be used to accumulate Fe in the plant parts using bacterial inoculation. For this, from a set of bacterial isolates, four Fe-tolerant bacteria were selected and identified based on 16S rRNA gene sequencing. The Fe-tolerant bacteria belonged to the genus Bacillus toyonensis (MG430287), Rhodococcus hoagii (MG432495), Lysinibacillus mangiferihumi (MG432492), and Lysinibacillus fusiformis (MG430290). Screening of plant growth-promoting properties of these isolates revealed that all isolates were able to produce indole acetic acid (50.0-84.0 μg/ml), siderophore, and potassium solubilization (except R. hoagii). Pot assay using Fe-contaminated ((8.07-8.35 g kg^-1) soils River Directorate of India) revealed that Fe-tolerant bacteria enhanced the growth of Brassica juncea and its biomass. Besides the improved plant growth, the inoculated plants also showed an overall percentage increase in the uptake of iron in root, stem, and leaf (57.91-128.31%) compared with uninoculated plants. In addition to enhanced plant growth attributes, the isolates also improved the total chlorophyll content and antioxidant properties such as total phenol, proline, and ascorbic acid oxidase. Thus, the results clearly indicated that these isolates could be used as a bioinoculant to improve the sequestration of Fe from the contaminated soils and alleviation of Fe stress in plants.

Alginate as a feature of osmotolerance differentiation among soil bacteria isolated from wild legumes growing in Portugal

Plants are naturally colonized by bacteria that can exert beneficial effects on growth and stress tolerance. These bacteria can be used as inoculants to boost crop productivity and plants resilience, and can be especially interesting if they are able to survive to abiotic stresses, such as drought. Herein we report the mechanisms that soil bacteria resort to tolerate drought and we also explore the influence of each mechanism to the level of drought tolerance exhibited, in order to test the hypothesis that different levels of tolerance displayed by bacteria are linked to differential efficiency of osmotolerance mechanisms. For this, the biochemical and physiological responses of bacterial strains of different genera and displaying different levels of tolerance to osmotic stress (sensitive, moderately tolerant and tolerant) induced by polyethylene glycol-6000 (PEG) were studied. Betaine, trehalose and alginate content increased in the majority of the strains exposed to PEG. Betaine was the osmolyte with higher increases, evidencing the important role of this compound in the tolerance of bacteria to drought. However, betaine and trehalose levels were not significantly different among bacteria with different osmotolerance levels. Several biochemical endpoints (protein content, superoxide dismutase, catalase, glutathione-S-transferases) related to oxidative stress were assessed, since oxidative damage has been reported in drought conditions, but little information is available. The oxidative stress parameters were not sufficient to explain differences in the osmotolerance observed for the tested strains. In contrast, alginate showed significant differences among the three levels of osmotolerance, linking the level of osmotolerance with the ability of soil bacteria to synthesize and accumulate alginate intracellularly for the first time. Moreover, our results show that this ability is present in different bacteria genera. Thus, evaluating the ability to synthesize alginate might be an important cue when considering bacterial inoculants for osmotically stressful conditions.

The influence of plant growth-promoting rhizobacteria in plant tolerance to abiotic stress: a survival strategy

Action is needed to face the global threat arising from inconsistent rainfall, rise in temperature, and salinization of farm lands which may be the product of climate change. As crops are adversely affected, man and animals may face famine. Plants are severely affected by abiotic stress (drought, salinity, alkalinity, and temperature), which impairs yield and results in loss to farmers and to the nation at large. However, microbes have been shown to be of great help in the fight against abiotic stress, via their biological activities at the rhizosphere of plants. The external application of chemical substances such as glycine betaine, proline, and nutrients has helped in sustaining plant growth and productive ability. In this review, we tried to understand the part played by bioinoculants in aiding plants to resist the negative consequences arising from abiotic stress and to suggest better practices that will be of help in today’s farming systems. The fact that absolute protection and sustainability of plant yield under stress challenges has not been achieved by microbes, nutrients, nor the addition of chemicals (osmo-protectants) alone suggests that studies should focus on the integration of these units (microbes, nutrients, chemical stimulants, and osmo-protectants) into a strategy for achieving a complete tolerance to abiotic stress. Also, other species of microbes capable of shielding plant from stress, boosting yield and growth, providing nutrients, and protecting the plants from harmful invading pathogens should be sought.