Insights into the Interactions among Roots, Rhizosphere, and Rhizobacteria for Improving Plant Growth and Tolerance to Abiotic Stresses: A Review

Impacts of fertilization methods on Salvia miltiorrhiza quality and characteristics of the epiphytic microbial community

Plant epiphytic microorganisms have established a unique symbiotic relationship with plants, which has a significant impact on their growth, immune defense, and environmental adaptation. However, the impact of fertilization methods on the epiphytic microbial community and their correlation with the yield and quality of medicinal plant was still unclear. In current study, we conducted a field fertilization experiment and analyzed the composition of epiphytic bacterial and fungal communities employing high throughput sequencing data in different organs (roots, stems, and leaves) of Salvia miltiorrhiza, as well as their correlation with plant growth. The results showed that fertilization significantly affected the active ingredients and hormone content, soil physicochemical properties, and the composition of epiphytic microbial communities. After fertilization, the plant surface was enriched with a core microbial community mainly composed of bacteria from Firmicutes, Proteobacteria, and Actinobacteria, as well as fungi from Zygomycota and Ascomycota. Additionally, plant growth hormones were the principal factors leading to alterations in the epiphytic microbial community of S. miltiorrhiza. Thus, the most effective method of fertilization involved the application of base fertilizer in combination with foliar fertilizer. This study provides a new perspective for studying the correlation between microbial community function and the quality of S. miltiorrhiza, and also provides a theoretical basis for the cultivation and sustainable development of high-quality medicinal plants.

Influence of Fertilization Methods and Types on Wheat Rhizosphere Microbiome Community and Functions

To investigate the effects of fertilization methods and types on wheat rhizosphere microorganisms, macroelement (N, K) and microelement (Zn) fertilizers were applied on wheat by foliar spraying (FS) and root irrigation (RI) methods in a field experiment. The results indicated that fertilization methods and types can have significant impacts on the diversity and structure of rhizospheric microorganisms in wheat. The application method produced more significant effects than the fertilizer type. RI-N played a more important role in improving the wheat yield and quality and affected the changes in some nitrogen-fixing bacterial communities. Finally, eight strains of bacteria belonging to Pseudomonas azotoformans and P. cedrina showed positive effects on the growth of wheat seedlings. Overall, our study provides a better understanding of the dynamics of wheat rhizosphere microbial communities and their relation to fertilization, yield, and quality, showing that plant growth-promoting rhizobacteria with nitrogen fixing may be a potential approach for more sustainable agriculture production.

Burkholderia ambifaria H8 as an effective biocontrol strain against maize stalk rot via producing volatile dimethyl disulfide

BACKGROUND

Maize stalk rot (MSR) caused by Fusarium graminearum is the primary factor contributing to the reduction in maize yield and quality. However, this soil-borne disease presents a significant challenge for sustainable control through field management and chemical agents. The screening of novel biocontrol agents can aid in developing innovative and successful strategies for MSR control.

RESULTS

A total of 407 strains of bacteria were isolated from the rhizosphere soil of a resistant maize inbred line. One strain exhibited significant antagonistic activity in plate and pot experiments, and was identified as Burkholderia ambifaria H8. The strain could significantly inhibit the mycelial growth and spore germination of F. graminearum, induce resistance to stalk rot, and promote plant growth. The volatile compounds produced by strain H8 and its secondary metabolites in the sterile fermentation broth exhibited antagonistic activity. The primary volatile compound produced by strain H8 was identified as dimethyl disulfide (DMDS) using gas chromatography tandem mass spectrometry. Through in vitro antagonistic activity assays and microscopic observation, it was confirmed that DMDS was capable of inhibiting mycelial growth and disrupting the mycelial structure of F. graminearum, suggesting it may be the major active compound for strain H8. The transcriptome data of F. graminearum further indicated that strain H8 and its volatile compounds could alter pathogenic fungi metabolism, influence the related metabolic pathways, and potentially induce cell apoptosis within F. graminearum.

CONCLUSION

Our results showed that B. ambifaria H8 was capable of producing the volatile substance dimethyl disulfide, which influenced the synthesis and permeability of cell membranes in pathogens. Thus, B. ambifaria H8 was found to be a promising biological control agent against MSR. © 2024 Society of Chemical Industry.

Effect of Bio-Fertilizer Application on Agronomic Traits, Yield, and Nutrient Uptake of Barley (Hordeum vulgare) in Saline Soil

Under salinity conditions, growth and productivity of grain crops decrease, leading to inhibition and limited absorption of water and elements necessary for plant growth, osmotic imbalance, ionic stress, and oxidative stress. Microorganisms in bio-fertilizers have several mechanisms to provide benefits to crop plants and reduce the harmful effect of salinity. They can be effective in dissolving phosphate, fixing nitrogen, promoting plant growth, and can have a combination of all these qualities. During two successful agricultural seasons, two field experiments were conducted to evaluate the effect of bio-fertilizer applications, including phosphate solubilizing bacteria (PSB), nitrogen fixation bacteria and a mix of phosphate-solubilizing bacteria and nitrogen fixation bacteria with three rates, 50, 75 and 100% NPK, of the recommended dose of minimal fertilizer on agronomic traits, yield and nutrient uptake of barley (Hordeum vulgare) under saline condition in Village 13, Farafra Oasis, New Valley Governorate, Egypt. The results showed that the application of Microbein + 75% NPK recorded the highest values of plant height, spike length, number of spikes/m2, grain yield (Mg ha-1), straw yield (Mg ha-1), biological yield (Mg ha-1), protein content %, nitrogen (N), phosphorus (P), potassium (K) uptakes in grain and straw (kg ha-1), available nitrogen (mg/kg soil), available phosphorus (mg/kg soil), total microbial count of soil, antioxidant activity of soil (AOA), dehydrogenase, nitrogen fixers, and PSB counts. The application of bio-fertilizers led to an increase in plant tolerance to salt stress, plant growth, grain yield, and straw yield, in addition to the application of the bio-fertilizers, which resulted in a 25% saving in the cost of mineral fertilizers used in barley production.

A biostimulant yeast, Hanseniaspora opuntiae, modifies Arabidopsis thaliana root architecture and improves the plant defense response against Botrytis cinerea

MAIN CONCLUSION

The biostimulant Hanseniaspora opuntiae regulates Arabidopsis thaliana root development and resistance to Botrytis cinerea. Beneficial microbes can increase plant nutrient accessibility and uptake, promote abiotic stress tolerance, and enhance disease resistance, while pathogenic microorganisms cause plant disease, affecting cellular homeostasis and leading to cell death in the most critical cases. Commonly, plants use specialized pattern recognition receptors to perceive beneficial or pathogen microorganisms. Although bacteria have been the most studied plant-associated beneficial microbes, the analysis of yeasts is receiving less attention. This study assessed the role of Hanseniaspora opuntiae, a fermentative yeast isolated from cacao musts, during Arabidopsis thaliana growth, development, and defense response to fungal pathogens. We evaluated the A. thaliana-H. opuntiae interaction using direct and indirect in vitro systems. Arabidopsis growth was significantly increased seven days post-inoculation with H. opuntiae during indirect interaction. Moreover, we observed that H. opuntiae cells had a strong auxin-like effect in A. thaliana root development during in vitro interaction. We show that 3-methyl-1-butanol and ethanol are the main volatile compounds produced by H. opuntiae. Subsequently, it was determined that A. thaliana plants inoculated with H. opuntiae have a long-lasting and systemic effect against Botrytis cinerea infection, but independently of auxin, ethylene, salicylic acid, or jasmonic acid pathways. Our results demonstrate that H. opuntiae is an important biostimulant that acts by regulating plant development and pathogen resistance through different hormone-related responses.

Unveiling the significance of rhizosphere: Implications for plant growth, stress response, and sustainable agriculture

In the rhizosphere, the activities within all processes and functions are primarily influenced by plant roots, microorganisms present in the rhizosphere, and the interactions between roots and microorganisms. The rhizosphere, a dynamic zone surrounding the roots, provides an ideal environment for a diverse microbial community, which significantly shapes plant growth and development. Microbial activity in the rhizosphere can promote plant growth by increasing nutrient availability, influencing plant hormonal signaling, and repelling or outcompeting pathogenic microbial strains. Understanding the associations between plant roots and soil microorganisms has the potential to revolutionize crop yields, improve productivity, minimize reliance on chemical fertilizers, and promote sustainable plant growth technologies. The rhizosphere microbiome could play a vital role in the next green revolution and contribute to sustainable and eco-friendly agriculture. However, there are still knowledge gaps concerning plant root-environment interactions, particularly regarding roots and microorganisms. Advances in metabolomics have helped to understand the chemical communication between plants and soil biota, yet challenges persist. This article provides an overview of the latest advancements in comprehending the communication and interplay between plant roots and microbes, which have been shown to impact crucial factors such as plant growth, gene expression, nutrient absorption, pest and disease resistance, and the alleviation of abiotic stress. By improving these aspects, sustainable agriculture practices can be implemented to increase the overall productivity of plant ecosystems.

Unveiling the potential of nanobubbles in water: Impacts on tomato's early growth and soil properties

Nanobubbles (NBs) in water have been proven to improve plant growth and seed germination, potentially reducing both water and fertilizer consumption. To unravel the promotion mechanism of NBs on plant growth, this study investigated the characteristics of NBs in tap water and their impacts on tomato's early growth, soil chemical properties, enzymatic activity and electrochemical properties of plant roots. Oxygen NBs (ONBs) were found to increase the seed germination by 10 % and plant growth by 30 %-50 % (e.g., stem and diameter), whereas nitrogen NBs (NNBs) only had a significant promotion (7 %-34 %) on plant height. Additionally, compared to control group, irrigation with ONBs increased the peroxidase activities by 500 %-1000 % in tomato leaves, which may increase the expression of genes for peroxidase and promote cell proliferation and plant growth. Moreover, electrical impedance spectroscopy (EIS) revealed that the ONBs could reduce the interfacial impedance due to the increased active surface area and electrical conductivity of root.

Comparative assessment of bacterial diversity and composition in arsenic hyperaccumulator, Pteris vittata L. and non-accumulator, Pteris ensiformis Burm

The use of arsenic (As) for various industrial and agricultural applications has led to worldwide environmental contamination. Phytoremediation using hyperaccumulators is a sustainable soil As mitigation strategy. Microbial processes play an important role in the tolerance and uptake of trace elements such as in plants. The rhizospheric and endophytic microbial communities are responsible for accelerating the mobility of trace elements around the roots and the production of plant growth-promoting compounds and enzymes. Several studies have reported that the As hyperaccumulator, Pteris vittata L. (PV) influences the microbial community in its rhizosphere and roots. Deciphering the differences in the microbiomes of hyperaccumulators and non-accumulators is crucial in understanding the mechanism of hyperaccumulation. We hypothesized that there are significant differences in the microbiome of roots, rhizospheric soil, and bulk soil between the hyperaccumulator PV and a non-accumulator of the same genus, Pteris ensiformis Burm. (PE), and that the differential recruitment of bacterial communities provides PV with an advantage in As contaminated soil. We compared root endophytic, rhizospheric, and bulk soil microbial communities between PV and PE species grown in As-contaminated soil in a greenhouse setting. There was a significant difference (p < 0.001) in the microbiome of the three compartments between the ferns. Differential abundance analysis showed 328 Amplicon Sequence Variants (ASVs) enriched in PV compared to 172 in PE. The bulk and rhizospheric soil of both ferns were abundant in As-resistant genera. However, As-tolerant root endophytic genera were present in PV but absent in PE. Our findings show that there is a difference between the bacterial composition of an As hyperaccumulator and a non-accumulator species grown in As-contaminated soil. These differences need to be further explored to develop strategies for improving the efficiency of metal uptake in plants growing in As polluted soil.

Organic Remobilization of zinc and phosphorus availability to plants by application of mineral solubilizing bacteria Pseudomonas aeruginosa

Incessant utilization of chemical fertilizers leads to the accumulation of minerals in the soil, rendering them unavailable to plants. Unaware of the mineral reserves present in the soil, farming communities employ chemical fertilizers once during each cultivation, a practice that causes elevated levels of insoluble minerals within the soil. The use of biofertilizers on the other hand, reduces the impact of chemical fertilizers through the action of microorganisms in the product, which dissolves minerals and makes them readily available for plant uptake, helping to create a sustainable environment for continuous agricultural production. In the current investigation, a field trial employing Arachis hypogaea L was conducted to evaluate the ability of Pseudomonas aeruginosa to enhance plant growth and development by solubilizing minerals present in the soil (such as zinc and phosphorus). A Randomized Complete Block Design (RCBD) included five different treatments as T1: Un inoculated Control; T2: Seeds treated with a liquid formulation of P. aeruginosa; T3: Seeds treated with a liquid formulation of P. aeruginosa and the soil amended with organic manure (farmyard); T4: Soil amended with organic manure (farmyard) alone; T5: Seeds treated with lignite (solid) based formulation of P. aeruginosa were used for the study. Efficacy was determined based on the plant's morphological characters and mineral contents (Zn and P) of plants and soil. Survival of P. aeruginosa in the field was validated using Antibiotic Intrinsic patterns (AIP). The results indicated that the combination treatment of P. aeruginosa liquid formulation and organic fertilizer (farmyard) (T3) produced the highest biometric parameters and mineral (Zn and P) content of the groundnut plants and the soil. This outcome is likely attributed to the mineral solubilizing capability of P. aeruginosa. Furthermore, the presence of farmyard manure increased the metabolic activity of P. aeruginosa by inducing its heterotrophic activity, leading to higher mineral content in T3 soil compared to other soil treatments. The AIP data confirmed the presence of the applied liquid inoculant by exhibiting a similar intrinsic pattern between the in vitro isolate and the isolate obtained from the fields. In summary, the Zn and P solubilization ability of P. aeruginosa facilitates the conversion of soil-unavailable mineral form into a form accessible to plants. It further proposes the utilization of the liquid formulation of P. aeruginosa as a viable solution to mitigate the challenges linked to solid-based biofertilizers and the reliance on mineral-based chemical fertilizers.

Mineral Solubilizing Rhizobacterial Strains Mediated Biostimulation of Rhodes Grass Seedlings

Minerals play a dynamic role in plant growth and development. However, most of these mineral nutrients are unavailable to plants due to their presence in fixed forms, which causes significant losses in crop production. An effective strategy to overcome this challenge is using mineral solubilizing bacteria, which can convert insoluble forms of minerals into soluble ones that plants can quickly assimilate, thus enhancing their availability in nutrient-depleted soils. The main objective of the present study was to isolate and characterize mineral solubilizing rhizobacteria and to assess their plant growth-promoting potential for Rhodes grass. Twenty-five rhizobacterial strains were isolated on a nutrient agar medium. They were characterized for solubilization of insoluble minerals (phosphate, potassium, zinc, and manganese), indole acetic acid production, enzymatic activities, and various morphological traits. The selected strains were also evaluated for their potential to promote the growth of Rhodes grass seedlings. Among tested strains, eight strains demonstrated strong qualitative and quantitative solubilization of insoluble phosphate. Strain MS2 reported the highest phosphate solubilization index, phosphate solubilization efficiency, available phosphorus concentration, and reduction in medium pH. Among tested strains, 75% were positive for zinc and manganese solubilization, and 37.5% were positive for potassium solubilization. Strain MS2 demonstrated the highest quantitative manganese solubilization, while strains MS7 and SM4 reported the highest solubilization of zinc and potassium through acidifying their respective media. The strain SM4 demonstrated the most increased IAA production in the presence and absence of L-tryptophan. The majority of strains were positive for various enzymes, including urease, catalase protease, and amylase activities. However, these strains were negative for coagulase activity except strains SM7 and MS7. Based on 16S rRNA gene sequencing, six strains, namely, SM2, SM4, SM5, MS1, MS2, and MS4, were identified as Bacillus cereus, while strains SM7 and MS7 were identified as Staphylococcus saprophyticus and Staphylococcus haemolyticus. These strains significantly improved growth attributes of Rhodes grass, such as root length, shoot length, and root and shoot fresh and dry biomasses compared to the uninoculated control group. The present study highlights the significance of mineral solubilizing and enzyme-producing rhizobacterial strains as potential bioinoculants to enhance Rhodes grass growth under mineral-deficient conditions sustainably.

Evaluating the potential of Bacillus licheniformis YZCUO202005 isolated from lichens in maize growth promotion and biocontrol

Lichens exist in an organismal organization of mycobiont, photobiont, and non-photoautotrophic bacteria. These organisms contribute to the growth of lichens even in poor nutrition substrates. However, studies on the isolation and application of non-photoautotrophic bacteria in plant growth and biocontrol are scanty. Therefore, a study was conducted to isolate and evaluate the potential of non-photoautotrophic bacteria from lichen tissues in maize plant growth promotion and biocontrol of plant pathogens (fungi and bacteria). Five bacterial strains were isolated and tested for their ability to produce indole-3-Acetic Acid (IAA). One bacterium named YZCUO202005 produced IAA, siderophores and biofilms, solubilized phosphate and potassium and exhibited extracellular enzymes (cellulases, proteases, amylase, and β -1,3-Glucanase). Based on the 16S rRNA sequence analysis results, YZCUO202005 was identified as Bacillus licheniformis. The strain inhibited the growth of five pathogenic fungi with an inhibition percent of between 58.7% and 71.7% and two pathogenic bacteria. Under greenhouse conditions, YZCUO202005 was tested for its abilities to enhance maize seed germination, and vegetative growth. Compared with the control treatment, the strain significantly enhanced the growth of stem length (i.e. 18 ± 0.64 cm, 78 ± 0.92 cm), leaf length (i.e. 10 ± 0.36 cm, 57 ± 1.42 cm), leaf chlorophyll levels (i.e., 13 ± 0.40, 40 ± 0.43 SPAD), and root length (i.e, 9.8 ± 2.25 cm, 22.5 ± 6.59 cm). Our results demonstrated that B. licheniformis YZCUO202005 from lichens has the potential to promote plant growth and reduce fungal and bacterial pathogens' growth. Furthermore, the results suggest that lichens are naturally rich sources of plant growth promotion and biocontrol agents that would be used in agriculture.

Recent advances in PGPR-mediated resilience toward interactive effects of drought and salt stress in plants

The present crisis at hand revolves around the need to enhance plant resilience to various environmental stresses, including abiotic and biotic stresses, to ensure sustainable agriculture and mitigate the impact of climate change on crop production. One such promising approach is the utilization of plant growth-promoting rhizobacteria (PGPR) to mediate plant resilience to these stresses. Plants are constantly exposed to various stress factors, such as drought, salinity, pathogens, and nutrient deficiencies, which can significantly reduce crop yield and quality. The PGPR are beneficial microbes that reside in the rhizosphere of plants and have been shown to positively influence plant growth and stress tolerance through various mechanisms, including nutrient solubilization, phytohormone production, and induction of systemic resistance. The review comprehensively examines the various mechanisms through which PGPR promotes plant resilience, including nutrient acquisition, hormonal regulation, and defense induction, focusing on recent research findings. The advancements made in the field of PGPR-mediated resilience through multi-omics approaches (viz., genomics, transcriptomics, proteomics, and metabolomics) to unravel the intricate interactions between PGPR and plants have been discussed including their molecular pathways involved in stress tolerance. Besides, the review also emphasizes the importance of continued research and implementation of PGPR-based strategies to address the pressing challenges facing global food security including commercialization of PGPR-based bio-formulations for sustainable agricultural.

Functional analysis of auxin derived from a symbiotic mycobiont

The biosynthesis of auxin or indole-3-acetic acid by microorganisms has a major impact on plant-microbe interactions. Several beneficial microbiota are known to produce auxin, which largely influences root development and growth in the host plants. Akin to findings in rhizobacteria, recent studies have confirmed the production of auxin by plant growth-promoting fungi too. Here, we show that Penicillium citrinum isolate B9 produces auxin as deduced by liquid chromatography tandem-mass spectrometry analysis. Such fungal auxin is secreted and contributes directly to enhanced root and shoot development and overall plant growth in Arabidopsis thaliana. Furthermore, auxin production by P. citrinum likely involves more than one tryptophan-dependent pathway. Using auxin biosynthesis inhibitor L-Kynurenine, we show that the indole-3-pyruvate pathway might be one of the key biosynthetic routes involved in such auxin production. Confocal microscopy of the DR5rev:GFP Arabidopsis reporter line helped demonstrate that P. citrunum B9-derived auxin is biologically active and is able to significantly enhance auxin signaling in roots during such improved root growth and plant development. Furthermore, the phenotypic growth defects arising from impaired auxin signaling in Arabidopsis taa1 mutant or upon L-Kynurenine treatment of wild-type Arabidopsis seedlings could be significantly alleviated by fungus B9-derived auxin, thus suggesting its positive role in plant growth promotion. Collectively, our results provide clear evidence that the production of auxin is one of the main mechanisms involved in induction of the beneficial plant growth by P. citrinum.

Metabolomics targets tissue-specific responses in alleviating the negative effects of salinity in tef (Eragrostis tef) during germination

MAIN CONCLUSION

Salinity induced metabolite responses resulted in differential accumulation of flavonoids and antioxidant metabolites in shoots and roots suggesting improved antioxidant capacity in providing salt-adaptive phenotype of tef seedling. Tef [(Eragrostis tef) (Zucc.) Trotter] is an important 'cash crop' of Ethiopia grown mainly for human food, and development of elite tef cultivars with better performance is vital to Ethiopian farmers and breeders. Soil salinity is one of the key constraints that affects tef yield in the Ethiopian lowlands and Rift valley where cultivation of tef is limited. Being a minor crop, the responses of tef towards salinity is unknown. Salinity involves physiological and metabolite reprogramming that can have major impact on germination and seedling establishment. Here we evaluate the in vitro effect of NaCl on tef germination and associate this with metabolomic approaches to suggest salt tolerance mechanisms. In this study, 19 tef varieties were screened for NaCl tolerance and were investigated using untargeted metabolomics. Screened tef varieties showed differential germination rates with NaCl treatment varying from < 20 to 100%. Viable seedlings exposed to NaCl exhibited purple-red pigment accumulation in the roots except for Beten and Tullu nasy varieties. Metabolite comparisons between shoots and roots showed significant differences and, in particular, roots of salt tolerant tef varieties accumulated flavonoid derivatives as well as sugars and cell wall associated metabolites. These metabolic changes were correlated with patterns of antioxidant capacities and total flavonoid content in shoots and roots and suggested a mitigating response by tef to salinity. Our study highlights the role of flavonoid accumulation following salt stress on tef seedlings and further these findings could be used as targets for selective tef breeding.

Biocontrol of fungal phytopathogens by Bacillus pumilus

Plant growth-promoting bacteria are one of the most interesting methods of controlling fungal phytopathogens. These bacteria can participate in biocontrol via a variety of mechanisms including lipopeptide production, hydrolytic enzymes (e.g., chitinase, cellulases, glucanase) production, microbial volatile organic compounds (mVOCs) production, and induced systemic resistance (ISR) triggering. Among the bacterial genera most frequently studied in this aspect are Bacillus spp. including Bacillus pumilus. Due to the range of biocontrol traits, B. pumilus is one of the most interesting members of Bacillus spp. that can be used in the biocontrol of fungal phytopathogens. So far, a number of B. pumilus strains that exhibit biocontrol properties against fungal phytopathogens have been described, e.g., B. pumilus HR10, PTB180, B. pumilus SS-10.7, B. pumilus MCB-7, B. pumilus INR7, B. pumilus SE52, SE34, SE49, B. pumilus RST25, B. pumilus JK-SX001, and B. pumilus KUDC1732. B. pumilus strains are capable of suppressing phytopathogens such as Arthrobotrys conoides, Fusarium solani, Fusarium oxysporum, Sclerotinia sclerotiorum, Rhizoctonia solani, and Fagopyrum esculentum. Importantly, B. pumilus can promote plant growth regardless of whether it alters the native microbiota or not. However, in order to increase its efficacy, research is still needed to clarify the relationship between the native microbiota and B. pumilus. Despite that, it can already be concluded that B. pumilus strains are good candidates to be environmentally friendly and commercially effective biocontrol agents.

Dynamic Responses of Rhizosphere Microorganisms to Biogas Slurry Combined with Chemical Fertilizer Application during the Whole Life Cycle of Rice Growth

Biogas slurry combined with chemical fertilizer (BCF) is widely used as a fertilizer in paddy fields and rhizosphere microorganisms are key players in plant growth and reproduction. However, the dynamic responses of rhizosphere microorganisms of field-grown rice to BCF application still remain largely unknown. In this study, a field experiment was conducted in two proximate paddy fields in Chongming Island to study the impacts of BCF on the changes in rhizosphere microorganisms during the whole rice growth, including seedling, tillering, booting, and grain-filling stages, with solely chemical fertilizer (CF) treatment as control. The results showed BCF could increase the N-, P-, and C- levels in paddy water as well as the rhizosphere microbial abundance and diversity compared with control. In particular, the phosphate-solubilizing- and cellulose-decomposing-bacteria (e.g., Bacillus) and fungi (e.g., Mortierella) were more abundant in the rhizosphere of BCF than those of CF. Moreover, these microbes increased markedly at the booting and grain-filling stages in BCF, which could promote rice to obtain available nutrients (P and C). It was noted that denitrifying-like bacteria (e.g., Steroidobacteraceae) decreased and dissimilatory nitrate reduction to ammonia-related bacteria (e.g., Geobacter, Anaeromyxobacter, and Ignavibacterium) increased at the booting and filling stages, which could promote N-availability. TP in paddy water of BCF was most correlated to the bacteria, while COD was the most critical regulator for the fungi. Furthermore, correlation network analysis showed nutrient-cycling-related microorganisms were more closely interconnected in BCF than those in CF. These findings showed the application of biogas slurry plus chemical fertilizer could regulate rhizosphere microorganisms towards a beneficial fertilizer use for rice growth.

No bacterial-mediated alleviation of thermal stress in a brown seaweed suggests the absence of ecological bacterial rescue effects

While microbiome alterations are increasingly proposed as a rapid mechanism to buffer organisms under changing environmental conditions, studies of these processes in the marine realm are lagging far behind their terrestrial counterparts. Here, we used a controlled laboratory experiment to examine whether the thermal tolerance of the brown seaweed Dictyota dichotoma, a common species in European coastal ecosystems, could be enhanced by the repeated addition of bacteria from its natural environment. Juvenile algae from three genotypes were subjected for two weeks to a temperature gradient, spanning almost the entire thermal range that can be tolerated by the species (11-30 °C). At the start of the experiment and again in the middle of the experiment, the algae were inoculated with bacteria from their natural environment or left untouched as a control. Relative growth rate was measured over the two-week period, and we assessed bacterial community composition prior to and at the end of the experiment. Since the growth of D. dichotoma over the full thermal gradient was not affected by supplementing bacteria, our results indicate no scope for bacterial-mediated stress alleviation. The minimal changes in the bacterial communities linked to bacterial addition, particularly at temperatures above the thermal optimum (22-23 °C), suggest the existence of a barrier to bacterial recruitment. These findings indicate that ecological bacterial rescue is unlikely to play a role in mitigating the effects of ocean warming on this brown seaweed.

Harnessing the efficacy of multifunctional rhizobacterial consortia for promoting the growth of Anethum graveolens L

Co-cultures of bacteria are more metabolically flexible and more tolerant to changes in the environment than single cultures. In order to test for plant growth promotion in a medicinal herb Anethum graveolens L, potent phosphate-solubilizing rhizobacteria were selected, characterized and assessed for their compatibility with each other. Molecular identification of isolates was made by 16s rRNA sequence, and they were identified as Pseudomonas aeruginosaNJC4 (OP289324), Serratia marcescens NJC21 (OP289323) and Bacillus spp. Dual species consortia, namely, Bacillus spp. + Serratia marcescens NJC21 (T1), and Pseudomonas aeruginosa NJC4 + Serratia marcescens NJC21 (T2), were tested for their ability to produce multiple plant beneficial activities such as phosphate solubilization, and ammonia and indole acetic acid production. The best isolate and consortium were evaluated for plant growth promotion activity. A plant treated with consortia T-2 seemed most effective in seed emergence at 84.66%, which was four times superior to the control. Growth and yield characters, along with all different rhizobacterial treatments, were examined by principal component analysis (PCA), where PC1 can explain 51.37% of the total variance and PC2 can explain 26.75%. PC1 was associated with wet biomass, chlorophyll b, and total chlorophyll content, which reflect the strong influence of consortia T-1. At the same time, PC2 was found to be related to dry biomass and chlorophyll a content. This study lends credence to the theory that microbial consortiums consisting of more than one efficient strains may be more effective than single cultures in boosting the increase of agricultural output in a sustainable way.

Effect of fertilization combination on cucumber quality and soil microbial community

Due to the lack of scientific guidance on the usage of fertilizer, the overuse of chemical and organic fertilizer is commonly witnessed all over the world, which causes soil degradation and leads to environmental pollution. The effect of fertilizer strategies on soil properties, cucumber nutrients, and microbial community was investigated in this study with the aim to explore an optimized and enhanced fertilizer strategy. There were five fertilizer strategies conducted including CK (no fertilizer), M (cow dung manure only), NPK (chemical fertilizer only), NPKM (chemical fertilizer combined with manure), and DNPKM (30%-reducing chemical fertilizer combined with manure). It was found that different fertilizer strategies significantly affected the soil organic matter and nutrient levels and cucumber production and nutrient contents of the experimental field. Different fertilizer strategies showed dramatic effects on the alpha- and beta-diversity of soil microbial communities. Moreover, NPKM and DNPKM groups could significantly improve the bacterial abundance and fungal diversity. In addition, the structure of microbial communities was significantly changed in the presence of manure, chemical fertilizer, and their combination. Optimized combination of NPK with M improved the abundance of aerobic, biofilm formation-related, and Gram-negative bacteria and suppressed the anaerobic and Gram-positive bacteria. The presence of saprotrophs fungi was enhanced by all fertilizer strategies, especially the plethora of Gymnoascus. The combination of manure with chemical fertilizer could improve the availability of nutrients, and therefore reduce the adverse effects and potential risks induced by excessive fertilizer application. In conclusion, the new fertilization approach can not only meet the growth requirements of cucumber after reduced fertilization, but also protect soil health, which provides a new candidate for the eco-friendly technology to satisfy the topic of carbon neutrality.

Antagonistic Strain Bacillus halotolerans Jk-25 Mediates the Biocontrol of Wheat Common Root Rot Caused by Bipolaris sorokiniana

Common root rot caused by Bipolaris sorokiniana infestation in wheat is one of the main reasons for yield reduction in wheat crops worldwide. The bacterium strain JK-25 used in the current investigation was isolated from wheat rhizosphere soil and was later identified as Bacillus halotolerans based on its morphological, physiological, biochemical, and molecular properties. The strain showed significant antagonism to B. sorokiniana, Fusarium oxysporum, Fusarium graminearum, and Rhizoctonia zeae. Inhibition of B. sorokiniana mycelial dry weight and spore germination rate by JK-25 fermentation supernatant reached 60% and 88%, respectively. The crude extract of JK-25 was found, by Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS), to contain the surfactin that exerted an inhibitory effect on B. sorokiniana. The disruption of mycelial cell membranes was observed under laser scanning confocal microscope (LSCM) after treatment of B. sorokiniana mycelium with the crude extract. The antioxidant enzyme activity of B. sorokiniana was significantly reduced and the oxidation product malondialdehyde (MDA) content increased after treatment with the crude extract. The incidence of root rot was significantly reduced in pot experiments with the addition of JK-25 culture fermentation supernatant, which had a significant biological control effect of 72.06%. Its ability to produce siderophores may help to promote wheat growth and the production of proteases and pectinases may also be part of the strain's role in suppressing pathogens. These results demonstrate the excellent antagonistic effect of JK-25 against B. sorokiniana and suggest that this strain has great potential as a resource for biological control of wheat root rot strains.

Optimistic contributions of plant growth-promoting bacteria for sustainable agriculture and climate stress alleviation

Global climate change is the major cause of abiotic and biotic stresses that have adverse effects on agricultural productivity to an irreversible level, thus threatening to limit gains in production and imperil sustainable agriculture. These climate change-induced abiotic stresses, especially saline, drought, extreme temperature, and so on affect plant morphological, physiological, biochemical, and metabolic characteristics through various pathways and mechanisms, ultimately hindering plant growth, development, and productivity. However, overuse and other inappropriate uses of agrochemicals are not conducive to the protection of natural resources and the environment, thus hampering sustainable agricultural development. With the vigorous development of modern agriculture, the application of plant growth-promoting bacteria (PGPB) can better ensure sustainable agriculture, due to their ability to improve soil properties and confer stress tolerance in plants. This review deciphered the underlying mechanisms of PGPB involved in enhancing plant stress tolerance and performance under various abiotic and biotic stresses. Moreover, the recent advancements in PGPB inoculation techniques, the commercialization of PGPB-based technology and the current applications of PGPB in sustainable agriculture were extensively discussed. Finally, an outlook on the future directions of microbe-aided agriculture was pointed out. Providing insights into plant-PGPB interactions under biotic and abiotic stresses and offering evidence and strategies for PGPB better commercialization and implementation can inspire the development of innovative solutions exploiting PGPB under climatological conditions.

Crop microbiome: their role and advances in molecular and omic techniques for the sustenance of agriculture

This review is an effort to provide in-depth knowledge of microbe's interaction and its role in crop microbiome using combination of advanced molecular and OMICS technology to translate this information for the sustenance of agriculture. Increasing population, climate change and exhaustive agricultural practices either influenced nutrient inputs of soil or generating biological and physico-chemical deterioration of the soils and affecting the agricultural productivity and agro-ecosystems. Alarming concerns toward food security and crop production claim for renewed attention in microbe-based farming practices. Microbes are omnipresent (soil, water, and air) and their close association with plants would help to accomplish sustainable agriculture goals. In the last few decades, the search for beneficial microbes in crop production, soil fertilization, disease management, and plant growth promotion is the thirst for eco-friendly agriculture. The crop microbiome opens new paths to utilize beneficial microbes and manage pathogenic microbes through integrated advanced biotechnology. The crop microbiome helps plants acquire nutrients, growth, resilience against phytopathogens, and tolerance to abiotic stresses, such as heat, drought, and salinity. Despite the emergent functionality of the crop microbiome as a complicated constituent of the plant fitness, our understanding of how the functionality of microbiome influenced by numerous factors including genotype of host, climatic conditions, mobilization of minerals, soil composition, nutrient availability, interaction between nexus of microbes, and interactions with other external microbiomes is partially understood. However, the structure, composition, dynamics, and functional contribution of such cultured and uncultured crop microbiome are least explored. The advanced biotechnological approaches are efficient tools for acquiring the information required to investigate the microbiome and extract data to develop high yield producing and resistant variety crops. This knowledge fills the fundamental gap between the theoretical concepts and the operational use of these advanced tools in crop microbiome studies. Here, we review (1) structure and composition of crop microbiome, (2) microbiome-mediated role associated with crops fitness, (3) Molecular and -omics techniques for exploration of crop microbiome, and (4) current approaches and future prospectives of crop microbiome and its exploitation for sustainable agriculture. Recent -omic approaches are influential tool for mapping, monitoring, modeling, and management of crops microbiome. Identification of crop microbiome, using system biology and rhizho-engineering, can help to develop future bioformulations for disease management, reclamation of stressed agro-ecosystems, and improved productivity of crops. Nano-system approaches combined with triggering molecules of crop microbiome can help in designing of nano-biofertilizers and nano-biopesticides. This combination has numerous merits over the traditional bioinoculants. They stimulate various defense mechanisms in plants facing stress conditions; provide bioavailability of nutrients in the soil, helps mitigate stress conditions; and enhance chances of crops establishment.

Photosynthesis under Biotic and Abiotic Environmental Stress

Photosynthesis is a unique process that has shaped life on our planet and created the conditions for all known life forms [...].

Piper caninum extract and Brevibacillus agri mixture suppresses rice leaf spot pathogen; Nigrospora oryzae and improves the production of red rice (Oryza sativa L)

Under the guise of enhancing productivity, using pesticides and artificial fertilizers in agriculture affects both the environment and living things. High chemical residues in food and the environment disrupt the health of consumers. One of the solutions that can bring about a reduction in the use of pesticides and chemicals is switching to organic fertilizers. The application of biopesticides originating from biological sources such as plant extracts and the use of microbes is gaining global acceptance. Therefore, this study aimed to obtain the best biopesticides and biostimulants that could suppress the leaf spot pathogen, Nigrospora oryzae, and increase the growth and yield of Bali red rice. The study contained four treatments, namely untreated control (F0), Piper caninum leaf extract (F1), Brevibacillus agri (F2), and fermented P. caninum leaf extract plus B. agri (F3). The treatments were arranged in a randomized complete block design, and each treatment was replicated three times. The parameters measured were the number of tillers per plant, number of leafs per plant, chlorophyll content, number of grains per panicle, grain weight, and grain yield. Furthermore, antimicrobial and antioxidants were assayed using SEM. GC-MS. At the end of the experiment, the disease index of the leaf spot was measured. The results showed that F3 significantly suppressed leaf spots caused by N. oryzae compared to other treatments, including untreated control in red rice. Additionally, the F3 significantly increased the number of productive tillers, number of grains per panicle, and grain yield compared to all other treatments. The F3 enhanced the crop yield at 6.19 tons/ha, an increase of 50% compared to the untreated control. The SEM.GC-MS results showed the presence of 2.3 butanediol, tetra-decanoic acid, butanoic acid, ethyl ester, benzene propanal, 3-(1,1-dimethylethyl)-a-methyl, a-N-Normethadol in treated plants with P. canicum plus B. agri.

Exploring the Plant Growth-Promotion of Four Streptomyces Strains from Rhizosphere Soil to Enhance Cucumber Growth and Yield

The genus Streptomyces is the most abundant and essential microbes in the soil microbial community. Streptomyces are familiar and have great potential to produce a large variety of bioactive compounds. This genus considers an efficient biofertilizer based on its plant growth-promoting activities. Based on their ability to produce a wide varieties of bioactive molecules, the present study aimed to explore the potential plant growth promotion of four Streptomyces strains and their role in enhancing cucumber growth and yield under greenhouse conditions. Streptomyces sp. strain HM2, Streptomyces thinghirensis strain HM3, Streptomyces sp. strain HM8, and Streptomyces tricolor strain HM10 were chosen for the current study. Plant growth-promoting (PGP) features, i.e., indole acetic acid (IAA) production, siderophore excretion, and solubilizing phosphate, were evaluated in vitro. All four strains produced IAA, siderophore, and immobilized inorganic phosphate. Following 4 days of incubation at 30 °C, strains HM2, HM3, HM8, and HM10 produced copious amounts of IAA (18, 22, 62, and 146 µg/mL, respectively) and siderophores (42.59, 40.01, 16.84, 64.14% SU, respectively). At the same time, P solubilization efficacy scored 64.3%, 84.4%, 57.2%, and 81.6% with the same frequency. During in planta evaluation, selected Streptomyces strains combined with rock phosphate were assessed as biofertilizers on the growth and yield of cucumber plants. Under all treatments, positive and significant differences in studied traits were manifested except dry stem matter (SDM), net assimilation rate (NAR), relative growth rate (RGR), and fruit firmness (FF). Treatment T4 (rock phosphate + strain HM3) followed by T5 (rock phosphate + strain HM8) revealed the best results for plant height (PH), number of leaves per plant (NLPP), root length (RL), number of fruits per plant (NFPP), fruit length (FL), fruit diameter (FD), fruit fresh weight per plant (FFWPP), soil P (SP) after 21 DAT, and soil P at the end of the experiment. Notably, T6 (rock phosphate + strain HM10) caused a considerable increase in leaf area (LA). Plant growth-promoting bacteria enhance plant growth and yield through phosphorus solubilizing, improve nutrient availability, produce phytohormones, and support plant growth under abiotic stress. These features are important for sustainable agriculture and reducing environmental pollution with chemical fertilizers and pesticides.

New insights into engineered plant-microbe interactions for pesticide removal

Over the past decades, rapid industrialization along with the overutilization of organic pollutants/pesticides has altered the environmental circumstances. Moreover, various anthropogenic, xenobiotics and natural activities also affected plants, soil, and human health, in both direct and indirect ways. To counter this, several conventional methods are currently practiced, but are uneconomical, noxious, and is yet inefficient for large-scale application. Plant-microbe interactions are mediated naturally in an ecosystem and are practiced in several areas. Plant growth promoting rhizobacteria (PGPR) possess certain attributes affecting plant and soil consequently performing decontamination activity via a direct and indirect mechanism. PGPR also harbors indispensable genes stimulating the mineralization of several organic and inorganic compounds. This makes microbes potential candidates for contributing to sustainably remediating the harmful pesticide contaminants. There is a limited piece of information about the plant-microbe interaction pertaining predict and understand the overall interaction concerning a sustainable environment. Therefore, this review focuses on the plant-microbe interaction in the rhizosphere and inside the plant's tissues, along with the utilization augmenting the crop productivity, reduction in plant stress along with decontamination of pesticides/organic pollutants in soil for sustainable environmental management.

Changes of endophytic microbial community in Rhododendron simsii roots under heat stress and its correlation with leaf physiological indicators

Introduction

The response mechanism of Rhododendron simsii and its endophytic microorganism to heat stress is still unclear.

Methods

The light incubator was used to set the temperature gradients, and the control (CK) was (day/night: 14/10 h) 25/22°C, the moderate-heat-stress (MHS) was 35/30°C and the high-heat-stress (HHS) was 40/35°C.

Results

Compared with CK, MHS significantly increased the contents of malondialdehyde, hydrogen peroxide, proline, and soluble sugar, as well as the activities of catalase and peroxidase in leaf, while HHS increased the activities of ascorbate peroxidase, and decreased chlorophyll content. Compared with CK, MHS reduced soil available nitrogen (N) content. Both heat stress changed the endophytic microbial community structure in roots. MHS enriched Pezicula and Paracoccus, while HHS significantly enriched Acidothermus and Haliangium. The abundance of Pezicula positively correlated with the contents of chlorophyll a and proline in leaf, and negatively correlated with soil ammonium N content. The abundance of Pezicula and Haliangium positively correlated with soluble sugar and malondialdehyde contents, respectively.

Conclusions

Our results suggest that root endophytic microorganisms play an important role in helping Rhododendron resisting heat stress, mainly by regulating soil N content and plant physiological characteristics.

Parthenium hysterophorus's Endophytes: The Second Layer of Defense against Biotic and Abiotic Stresses

Parthenium hysterophorus L. is considered an obnoxious weed due to its rapid dispersal, fast multiplications, and agricultural and health hazards. In addition to its physio-molecular and phytotoxic allelochemical usage, this weed most probably uses endophytic flora as an additional line of defense to deal with stressful conditions and tolerate both biotic and abiotic stresses. The aim of this article is to report the diversity of endophytic flora (fungi and bacteria) in P. hysterophorus and their role in the stress mitigation (biotic and abiotic) of other important crops. Various endophytes were reported from P.&nbsp;hysterophorus and their roles in crops evaluated under biotic and abiotic stressed conditions. These endophytes have the potential to alleviate different stresses by improving crops/plants growth, development, biomass, and photosynthetic and other physiological traits. The beneficial role of the endophytes may be attributed to stress-modulating enzymes such as the antioxidants SOD, POD and APX and ACC deaminases. Additionally, the higher production of different classes of bioactive secondary metabolites, i.e., flavonoids, proline, and glutathione may also overcome tissue damage to plants under stressed conditions. Interestingly, a number of medicinally important phytochemicals such as anhydropseudo-phlegmcin-9, 10-quinone-3-amino-8-O methyl ether 'anhydropseudophlegmacin-9, 10-quinone-3-amino-8-Omethyl ether were reported from the endophytic flora of P. hysterophorus. Moreover, various reports revealed that fungal and bacterial endophytes of P. hysterophorus enhance plant growth-promoting attributes and could be added to the consortium of biofertilizers.

Optimization and identification of siderophores produced by Pseudomonas monteilii strain MN759447 and its antagonism toward fungi associated with mortality in Dalbergia sissoo plantation forests

Siderophore-positive bacteria present in the rhizosphere and in bulk soil assist plants by either inhibiting phytopathogen proliferation or increasing plant growth. The bacterial diversity of the Shisham forest ecosystem in the Tarai region of the Western Himalayas was studied and used for siderophore production, taking into account the large-scale dieback and wilt-induced mortality in Dalbergia sissoo (common name: shisham) plantation forests and the importance of soil microbes in tree health. In addition, Pseudomonas, Burkholderia, and Streptomyces were prominent siderophore-positive bacteria in Shisham forests. Pseudomonas species are known for their remarkable siderophore-producing ability. Bacterial siderophores inhibit pathogen growth by rapidly lowering the number of ferric ions in the rhizosphere. The Pseudomonas monteilii strain MN759447 was isolated from a D. sissoo plantation forest at the Agroforestry Research Centre, Pantnagar, Uttarakhand (28°58'N 79°25'E/28.97°N 79.41°E). It produces a significant number of siderophore units (80.36% in total). A two-stage optimization of growth factors was attempted in the strain MN759447 for better siderophore recovery. In the first-stage single-factor experiment, among the five variables studied, only pH, NH₄NO₃ concentration, and Fe concentration affected siderophore synthesis. In the second stage, an optimization of pH, NH₄NO₃ concentration, and Fe concentration for improved growth and enhanced siderophore production was carried out using a Box-Behnken design with response surface methodology. By using LC-MS, two derivatives of pseudomonine, salicylic acid, and kynurenic acid were detected as siderophores in the purified XAD-2 methanol extract of the P. monteilii strain MN759447. In addition to siderophore production, the P. monteilii strain MN759447 also exhibited a broad range of antagonistic activity against Aspergillus calidoustus (65%), Fusarium oxysporum (41.66%), Talaromyces pinophilus (65%), and Talaromyces verruculosus (65.1%) that are linked to sissoo mortality. To our knowledge, this is the first report on siderophore-producing bacteria isolated, identified, and characterized from the D. sissoo Roxb. forest habitat. This strain can also be developed as a commercial product.

Induction of resilience strategies against biochemical deteriorations prompted by severe cadmium stress in sunflower plant when Trichoderma and bacterial inoculation were used as biofertilizers

Background

Cadmium (Cd) is a highly toxic heavy metal. Its emission is suspected to be further increased due to the dramatic application of ash to agricultural soils and newly reclaimed ones. Thereby, Cd stress encountered by plants will exacerbate. Acute and chronic exposure to Cd can upset plant growth and development and ultimately causes plant death. Microorganisms as agriculturally important biofertilizers have constantly been arising as eco-friendly practices owing to their ability to built-in durability and adaptability mechanisms of plants. However, applying microbes as a biofertilizer agent necessitates the elucidation of the different mechanisms of microbe protection and stabilization of plants against toxic elements in the soil. A greenhouse experiment was performed using Trichoderma harzianum and plant growth-promoting (PGP) bacteria (Azotobacter chroococcum and Bacillus subtilis) individually and integrally to differentiate their potentiality in underpinning various resilience mechanisms versus various Cd levels (0, 50, 100, and 150 mg/kg of soil). Microorganisms were analyzed for Cd tolerance and biosorption capacity, indoleacetic acid production, and phosphate and potassium solubilization in vitro. Plant growth parameters, water relations, physiological and biochemical analysis, stress markers and membrane damage traits, and nutritional composition were estimated.

Results

Unequivocal inversion from a state of downregulation to upregulation was distinct under microbial inoculations. Inoculating soil with T. harzianum and PGPB markedly enhanced the plant parameters under Cd stress (150 mg/kg) compared with control plants by 4.9% and 13.9%, 5.6% and 11.1%, 55.6% and 5.7%, and 9.1% and 4.6% for plant fresh weight, dry weight, net assimilation rate, and transpiration rate, respectively; by 2.3% and 34.9%, 26.3% and 69.0%, 26.3% and 232.4%, 135.3% and 446.2%, 500% and 95.6%, and 60% and 300% for some metabolites such as starch, amino acids, phenolics, flavonoids, anthocyanin, and proline, respectively; by 134.0% and 604.6% for antioxidants including reduced glutathione; and by 64.8% and 91.2%, 21.9% and 72.7%, and 76.7% and 166.7% for enzymes activity including ascorbate peroxidase, glutathione peroxidase, and phenylalanine ammonia-lyase, respectively. Whereas a hampering effect mediated by PGP bacterial inoculation was registered on levels of superoxide anion, hydroxyl radical, electrolyte leakage, and polyphenol oxidase activity, with a decrease of 0.53%, 14.12%, 2.70%, and 5.70%, respectively, under a highest Cd level (150 mg/kg) compared with control plants. The available soil and plant Cd concentrations were decreased by 11.5% and 47.5%, and 3.8% and 45.0% with T. harzianum and PGP bacterial inoculation, respectively, compared with non-inoculated Cd-stressed plants. Whereas, non-significant alternation in antioxidant capacity of sunflower mediated by T. harzianum action even with elevated soil Cd concentrations indicates stable oxidative status. The uptake of nutrients, viz., K, Ca, Mg, Fe, nitrate, and phosphorus, was interestingly increased (34.0, 4.4, 3.3, 9.2, 30.0, and 1.0 mg/g dry weight, respectively) owing to the synergic inoculation in the presence of 150 mg of Cd/kg.

Conclusions

However, strategies of microbe-induced resilience are largely exclusive and divergent. Biofertilizing potential of T. harzianum showed that, owing to its Cd biosorption capability, a resilience strategy was induced via reducing Cd bioavailability to be in the range that turned its effect from toxicity to essentiality posing well-known low-dose stimulation phenomena (hormetic effect), whereas using Azotobacter chroococcum and Bacillus subtilis, owing to their PGP traits, manifested a resilience strategy by neutralizing the potential side effects of Cd toxicity. The synergistic use of fungi and bacteria proved the highest efficiency in imparting sunflower adaptability under Cd stress.

Drought and global hunger: biotechnological interventions in sustainability and management

Drought may be efficiently managed using the following strategies: prevention, mitigation, readiness, recovery, and transformation. Biotechnological interventions may become highly important in reducing plants' drought stress in order to address key plant challenges such as population growth and climate change. Drought is a multidimensional construct with several triggering mechanisms or contributing factors working at various spatiotemporal scales, making it one of the known natural catastrophes. Drought is among the causes of hunger and malnutrition, decreasing agricultural output, and poor nutrition. Many deaths caused in children are due to hunger situations, and one in four children face stunted growth. All this hunger and malnutrition may be responsible for the reduction in agricultural productivity caused due to the drought situations affecting food security. Global Hunger Index has been accelerating due to under-nutrition and under-5 deaths. Drought has been covering more than 20% of the world's agricultural areas, leading to significantly less food production than what is required for consumption. Drought reduces soil fertility and adversely affects soil biological activity reducing the inherent capacity of the soil to support vegetation. Recent droughts have had a much greater effect on people's lives, even beyond causing poverty and hunger. Drought may have substantial financial consequences across the globe it may cause a severe impact on the world economy. It is a natural feature of the environment that will appear and disappear as it has in history. Due to increasing temperatures and growing vulnerabilities, it will undoubtedly occur more often and seriously in the coming years. To ensure sustainable socio-economic and social development, it is critical to reducing the effects of potential droughts worldwide using different biotechnological interventions. It's part of a long-term growth plan, and forecasting is essential for early warnings and global hunger management.

Insight into Recent Progress and Perspectives in Improvement of Antioxidant Machinery upon PGPR Augmentation in Plants under Drought Stress: A Review

Agriculture has a lot of responsibility as the rise in the world’s population demands more food requirements. However, more than one type of biotic and abiotic stress continually impacts agricultural productivity. Drought stress is a major abiotic stress that significantly affects agricultural productivity every year as the plants undergo several morphological, biochemical, and physiological modifications, such as repressed root and shoot growth, reduced photosynthesis and transpiration rate, excessive production of reactive oxygen species (ROS), osmotic adjustments, and modified leaf senescence regulating and stress signaling pathways. Such modifications may permanently damage the plants; therefore, mitigation strategies must be developed. The use of drought resistant crop cultivars is more expensive and labor-intensive with few advantages. However, exploiting plant growth promoting rhizobacteria (PGPR) is a proven alternative with numerous direct and indirect advantages. The PGPR confers induced systemic tolerance (IST) mechanisms in plants in response to drought stress via multiple mechanisms, including the alteration of root architecture, maintenance of high relative water content, improvement of photosynthesis rate, production of phytohormones, exopolysaccharides, ACC deaminase, carotenoids and volatiles, induction of antioxidant defense system, and alteration in stress-responsive gene expression. The commercial application of PGPR as bioinoculants or biostimulants will remain contingent on more robust strain selection and performance under unfavorable environmental conditions. This review highlights the possible mechanisms of PGPR by activating the plant adaptive defense systems for enhancing drought tolerance and improving overall growth and yield.

Enhancing quinoa growth under severe saline-alkali stress by phosphate solubilizing microorganism Penicillium funicuiosum P1

Promoting the growth of plants and improving plant stress-resistance by plant growth-promoting microorganism increasingly become a hotpot. While, most researchers focus on their supply role of nutrition or plant hormone. In this study, a novel mechanism that phosphate solubilizing microorganisms promoted plant growth under saline-alkali stress through secretion of organic acids, was proposed. The effects of desulfurization gypsum, humic acid, organic fertilizer and phosphate-solubilizing microorganism Penicillium funicuiosum P1 (KX400570) on the growth of quinoa (Chenopodium quinoa cv. Longli 1), showed that the survival rate, stem length and dry weight of quinoa treated with P1 were 2.5, 1.5, 1 and 1.5 times higher than those of sterile water (CK) under severe saline-alkali stress. The growth-promoting effect of P1 on quinoa was much better than that of other treatment groups. In addition, P1 promoted the growth of quinoa because the organic acids (malic acid, citric acid, succinic acid, etc.) from P1 stimulated the antioxidant system and promote the photosynthesis of quinoa, further promote quinoa growth.

Plant Growth-Promoting Bacterial Consortia as a Strategy to Alleviate Drought Stress in Spinacia oleracea

Drought stress is one of the most severe abiotic stresses affecting soil fertility and plant health, and due to climate change, it is destined to increase even further, becoming a serious threat to crop production. An efficient, eco-friendly alternative is the use of plant growth-promoting bacteria (PGPB), which can promote plant fitness through direct and indirect approaches, protecting plants from biotic and abiotic stresses. The present study aims to identify bacterial consortia to promote Spinacia oleracea L. cv Matador’s seed germination and protect its seedlings from drought stress. Eight PGPB strains belonging to the Bacillus, Azotobacter, and Pseudomonas genera, previously characterized in physiological conditions, were analyzed under water-shortage conditions, and a germination bioassay was carried out by biopriming S. oleracea seeds with either individual strains or consortia. The consortia of B. amyloliquefaciens RHF6, B. amyloliquefaciens LMG9814, and B. sp. AGS84 displayed the capacity to positively affect seed germination and seedlings’ radical development in both standard and drought conditions, ameliorating the plants’ growth rate compared to the untreated ones. These results sustain using PGPB consortia as a valid ameliorating water stress strategy in the agro-industrial field.

Production of extracellular amylase contributes to the colonization of Bacillus cereus 0-9 in wheat roots

Background

Bacteria usually secrete a variety of extracellular enzymes to degrade extracellular macromolecules to meet their nutritional needs and enhance their environmental adaptability. Bacillus cereus 0–9, a biocontrol bacterial strain isolated from wheat roots, has three genes annotated as encoding amylases in the genome, but their functions are unknown, and whether they are involved in the colonization process of the bacterium remains to be further studied.

Methods

Mutant gene strains and fluorescently tagged strains were constructed by homologous recombination, and amylase protein was expressed in the prokaryotic Escherichia coli BL21(DE3) expression system. The iodine staining method was used to measure the activity of amylase proteins. We further observed the colonization abilities of the test strains in wheat roots through frozen section technology.

Results

The results showed that there were three amylase-encoding genes, amyC, amyP and amyS, in the B. cereus 0–9 genome. Among the three amylase encoding genes, only amyS produced extracellular amylase whose secretion was related to signal peptide at position 1–27. The AmyS protein encoded by the amyS gene is an α-amylase. The growth of Rhizoctonia cerealis was inhibited 84.7% by B. cereus 0–9, but the biocontrol ability of the ΔamyS strain decreased to 43.8% and that of ΔamyS/amyS was restored when the amyS gene was complemented. Furthermore, the biocontrol ability of the ΔamySec strain was decreased to 46.8%, almost the same as that of the ΔamyS mutant. Due to the deletion of the amyS gene, the colonization capacities of ΔamyS (RFP) and ΔamySec (RFP) in wheat roots decreased, while that of ΔamyS/amyS (RFP) was restored after the amyS gene was complemented, indicating that the amyS gene influences the colonization of B. cereus 0–9 in wheat roots. In addition, the colonization and biocontrol abilities of the mutant were restored after the addition of sugars, such as glucose and maltose.

Conclusions

B. cereus 0–9 encodes three genes annotated as amylases, amyC, amyP and amyS. Only the deletion of the amyS gene with a signal peptide did not produce extracellular amylase. The AmyS protein encoded by the amyS gene is an α-amylase. Our results indicated that the amyS gene is closely related to the colonization abilities of B. cereus 0–9 in wheat roots and the biocontrol abilities of B. cereus 0–9 to fight against R. cerealis. The extracellular amylase produced by B. cereus 0–9 can hydrolyze starch and use glucose, maltose and other nutrients to meet the needs of bacterial growth. Therefore, it is very possible that the secretion and hydrolytic activities of extracellular amylase can promote the colonization of B. cereus 0–9 in wheat roots and play important roles in the prevention and control of plant diseases. Our results contribute to exploring the mechanisms of microbial colonization in plant roots.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02618-7.

Unraveling the tripartite interaction of volatile compounds of Streptomyces rochei with grain mold pathogens infecting sorghum

Sorghum is a major grain crop used in traditional meals and health drinks, and as an efficient fuel. However, its productivity, value, germination, and usability are affected by grain mold, which is a severe problem in sorghum production systems, which reduces the yield of harvested grains for consumer use. The organic approach to the management of the disease is essential and will increase consumer demand. Bioactive molecules like mVOC (volatile organic compound) identification are used to unravel the molecules responsible for antifungal activity. The Streptomyces rochei strain (ASH) has been reported to be a potential antagonist to many pathogens, with high levels of VOCs. The present study aimed to study the inhibitory effect of S. rochei on sorghum grain mold pathogens using a dual culture technique and via the production of microbial volatile organic compounds (mVOCs). mVOCs inhibited the mycelial growth of Fusarium moniliforme by 63.75 and Curvularia lunata by 68.52%. mVOCs suppressed mycelial growth and inhibited the production of spores by altering the structure of mycelia in tripartite plate assay. About 45 mVOCs were profiled when Streptomyces rochei interacted with these two pathogens. In the present study, several compounds were upregulated or downregulated by S. rochei, including 2-methyl-1-butanol, methanoazulene, and cedrene. S. rochei emitted novel terpenoid compounds with peak areas, such as myrcene (1.14%), cymene (6.41%), and ç-terpinene (7.32%) upon interaction with F. moniliforme and C. lunata. The peak area of some of the compounds, including furan 2-methyl (0.70%), benzene (1.84%), 1-butanol, 2-methyl-(8.25%), and myrcene (1.12)%, was increased during tripartite interaction with F. moniliforme and C. lunata, which resulted in furan 2-methyl (6.60%), benzene (4.43%), butanol, 2-methyl (18.67%), and myrcene (1.14%). These metabolites were implicated in the sesquiterpenoid and alkane biosynthetic pathways and the oxalic acid degradation pathway. The present study shows how S. rochei exhibits hyperparasitism, competition, and antibiosis via mVOCs. In addition to their antimicrobial functions, these metabolites could also enhance plant growth.

Okra Growth, Yield and Rhizosphere Microbiome Responses to the Encapsulated Bioinoculant Application under Reduced Fertilization Regime

There is limited evidence that Enterobacter hormaechei can improve plant physiology and yield through soil phosphate (P) and potassium (K) amelioration. This study unraveled the effect of different soil inoculation methods i.e., free-cell and encapsulated (alginate bead containing sugar-protein hydrolysate and molasses) E. hormaechei 40a with different rates of PK-fertilization on okra P and K uptake, and soil rhizosphere bacterial community. The results revealed that 3HB (half-dose PK-fertilizer + encapsulated strain 40a) had the highest soil available P (SAP) and K (SAK), as well as P and K uptake for all plant organs, followed by 3F (full-dose PK-fertilizer), 3HI (half-dose PK-fertilizer + free-cell strain 40a), and 3H (half-dose PK-fertilizer), and improved yield by up to 75.6%. Both inoculated and full-dose fertilizer treatments produced larger pods (>15 cm) compared to 3H. We discovered increased bacterial richness and diversity in both 3HB and 3HI samples compared to uninoculated treatments. Both 3HB and 3F treatments were positively correlated with the increasing abundance of Acidobacteriales, Burkholderia caballeronia paraburkholderia, Gemmataceae, and Sphingomonas along with the SAP and SAK. The plant-beneficial effect of one-time 3HB treatment on okra growth and yield was comparable to biweekly inoculation in 3HI, suggesting a new cost-effective farming approach in precision agriculture.

Efficacy of biological agents and fillers seed coating in improving drought stress in anise

Many plants, including anise, have tiny, non-uniform seeds with low and light nutrient reserves. The seeds also show a weak establishment, especially under stressful conditions where their accurate planting in the soil and optimal yield are tough. This study sought to improve anise seeds' physical and physiological characteristics under drought stress. To this end, two factorial experiments under laboratory and greenhouse conditions were performed in a completely randomized design with 4 and 3 replications, respectively. Five levels of seed inoculation (inoculation with T36 and T43 of Trichoderma harzianum, and CHA0 and B52 of Pseudomonas fluorescent, and non-inoculation which means that control seeds were not treated with microbial inoculant), three levels of coating (K10P20, K10P10V5, and non-coating), and three levels of drought stress (0, -3, and -6 bars) were considered as the factorial experiment [vermiculite (V), kaolin (K), and perlite (P) numbers refer to the amount of material used in grams]. The laboratory experiment revealed that the combined treatments of bio-agents with coating increased the physical and germination characteristics of anise seeds compared to the control treatment. The greenhouse experiment showed that drought stress reduced the initial growth indices. Still, the combination treatments of biological agents and coating (fillers) could alleviate the destructive effects of drought stress to some extent and improve these indices. The best treatment was provided by T36 and K10P20 in both experiments, which significantly increased morphological indices.

Co-inoculation of biochar and arbuscular mycorrhizae for growth promotion and nutrient fortification in soybean under drought conditions

Drought is significant abiotic stress that affects the development and yield of many crops. The present study is to investigate the effect of arbuscular mycorrhizal fungi (AMF) and biochar on root morphological traits, growth, and physiological traits in soybean under water stress. Impact of AMF and biochar on development and root morphological traits in soybean and AMF spores number and the soil enzymes' activities were studied under drought conditions. After 40 days, plant growth parameters were measured. Drought stress negatively affected soybean growth, root parameters, physiological traits, microbial biomass, and soil enzyme activities. Biochar and AMF individually increase significantly plant growth (plant height, root dry weight, and nodule number), root parameters such as root diameter, root surface area, total root length, root volume, and projected area, total chlorophyll content, and nitrogen content in soybean over to control in water stress. In drought conditions, dual applications of AMF and biochar significantly enhanced shoot and root growth parameters, total chlorophyll, and nitrogen contents in soybean than control. Combined with biochar and AMF positively affects AMF spores number, microbial biomass, and soil enzyme activities in water stress conditions. In drought stress, dual applications of biochar and AMF increase microbial biomass by 28.3%, AMF spores number by 52.0%, alkaline phosphomonoesterase by 45.9%, dehydrogenase by 46.5%, and fluorescein diacetate by 52.2%, activities. The combined application of biochar and AMF enhance growth, root parameters in soybean and soil enzyme activities, and water stress tolerance. Dual applications with biochar and AMF benefit soybean cultivation under water stress conditions.

Halotolerant Plant Growth-Promoting Rhizobacteria Isolated From Saline Soil Improve Nitrogen Fixation and Alleviate Salt Stress in Rice Plants

Salinity is one of the most damaging abiotic stresses due to climate change impacts that affect the growth and yield of crops, especially in lowland rice fields and coastal areas. This research aimed to isolate potential halotolerant plant growth-promoting rhizobacteria from different rhizo-microbiome and use them as effective bioinoculants to improve rice growth under salinity stress conditions. Bioassay using rice seedlings was performed in a randomized block design consisting of 16 treatments (control and 15 bacterial isolates) with three replications. Results revealed that isolates S3, S5, and S6 gave higher shoot height, root length, and plant dry weight compared with control (without isolates). Based on molecular characteristics, isolates S3 and S5 were identified as Pseudomonas stutzeri and Klebsiella pneumonia. These isolates were able to promote rice growth under salinity stress conditions as halotolerant plant growth-promoting rhizobacteria. These three potent isolates were found to produce indole-3-acetic acid and nitrogenase.

Insight into soil nitrogen and phosphorus availability and agricultural sustainability by plant growth-promoting rhizobacteria

Nitrogen and phosphorus are critical for the vegetation ecosystem and two of the most insufficient nutrients in the soil. In agriculture practice, many chemical fertilizers are being applied to soil to improve soil nutrients and yield. This farming procedure poses considerable environmental risks which affect agricultural sustainability. As robust soil microorganisms, plant growth-promoting rhizobacteria (PGPR) have emerged as an environmentally friendly way of maintaining and improving the soil's available nitrogen and phosphorus. As a special PGPR, rhizospheric diazotrophs can fix nitrogen in the rhizosphere and promote plant growth. However, the mechanisms and influences of rhizospheric nitrogen fixation (NF) are not well researched as symbiotic NF lacks summarizing. Phosphate-solubilizing bacteria (PSB) are important members of PGPR. They can dissolve both insoluble mineral and organic phosphate in soil and enhance the phosphorus uptake of plants. The application of PSB can significantly increase plant biomass and yield. Co-inoculating PSB with other PGPR shows better performance in plant growth promotion, and the mechanisms are more complicated. Here, we provide a comprehensive review of rhizospheric NF and phosphate solubilization by PGPR. Deeper genetic insights would provide a better understanding of the NF mechanisms of PGPR, and co-inoculation with rhizospheric diazotrophs and PSB strains would be a strategy in enhancing the sustainability of soil nutrients.

Genomic and Phenotypic Insights into the Potential of Bacillus subtilis YB-15 Isolated from Rhizosphere to Biocontrol against Crown Rot and Promote Growth of Wheat

Simple Summary

Biological control of plant diseases caused by fungal pathogens using antagonistic microorganisms including Bacilli has been considered to be an effective and safe alternative to chemical fungicides. Fusarium crown rot of wheat is a serious fungal disease affecting yield and grain quality. In this study, a newly isolated strain of Bacillus subtilis YB-15 from soil of wheat rhizosphere significantly inhibited Fusarium crown rot as well as improved growth of wheat seedlings. Multiple potential biocontrol and growth-promoting attributes of Bacillus subtilis YB-15 were determined in vitro and according to the whole genome sequencing analysis. Overall, the results demonstrated that Bacillus subtilis YB-15 has great potential for practical application in controlling plant fungal diseases and improving plant growth.

Abstract

Fusarium crown rot caused by Fusarium pseudograminearum is one of the most devastating diseases of wheat worldwide causing major yield and economic losses. In this study, strain YB-15 was isolated from soil of wheat rhizosphere and classified as Bacillus subtilis by average nucleotide identity analysis. It significantly reduced Fusarium crown rot with a control efficacy of 81.50% and significantly improved the growth of wheat seedlings by increasing root and shoot fresh weight by 11.4% and 4.2%, respectively. Reduced Fusarium crown rot may have been due to direct antagonism by the production of β-1, 3-glucanase, amylase, protease and cellulase, or by the ability of B. subtilis YB-15 to induce defense-related enzyme activities of wheat seedlings, both alone and in seedlings infected with F. pseudograminearum. Improved plant growth may be related to the ability of B. subtilis YB-15 to secrete indole acetic acid and siderophores, as well as to solubilize phosphorus. In addition, the genome of strain YB-15 was determined, resulting in a complete assembled circular genome of 4,233,040 bp with GC content of 43.52% consisting of 4207 protein-encoding genes. Sequencing the B. subtilis YB-15 genome further revealed genes for encoding carbohydrate-active enzymes, biosynthesis of various secondary metabolites, nutrient acquisition, phytohormone production, chemotaxis and motility, which could explain the potential of strain YB-15 to be plant growth-promoting bacteria and biological control agent. B. subtilis YB-15 appears to be a promising biocontrol agent against Fusarium crown rot as well as for wheat growth promotion.

Effects of Vermicompost Substrates and Coconut Fibers Used against the Background of Various Biofertilizers on the Yields of Cucumis melo L. and Solanum lycopersicum L

Vermicompost has been promoted as a viable substrate component owing to its physicochemical properties, nutrient richness, and status as an excellent soil improver. It is considered the best organic fertilizer and is more eco-friendly than chemical fertilizers. Plant-growth-promoting microorganisms (PGPMs) are defined as plant biofertilizers that improve nutritional efficiency—that is, they transform nutrients within substrates from organic to inorganic forms, making them available for plants. The main objective of this research study is to evaluate the effects of the application of three PGPM microbial consortia on different mixtures of organic substrates based on vermicompost (V) and coconut fiber (CF) on two different horticultural crops. We performed a yield analysis and drainage nutrient tests and determined the plant nutritional status and enzymatic activity in organic substrates based on the two crops, Cucumis melo L. and Solanum lycopersicum L. A multivariate analysis of variance and principal component analysis was conducted using substrate types and PGPMs as factors. Differences (p < 0.05) in yield, dehydrogenase activity, the nutrient concentrations in a petiole sap, and drainage were observed at 30, 60, 75, and 90 days after transplant. PGPMs such as Trichoderma sp. and plant-growth-promoting rhizobacteria (PGPR) in organic substrates (40V + 60CF) can significantly improve the nutritional status of plants for use in organic soilless container agriculture. Biofertilization with PGPMs and suitable mixtures of organic substrates together with aqueous extracts (tea) of vermicompost, as nutrient solutions applied by fertigation, has allowed us to achieve an adequate level of production through environmentally friendly techniques. The results obtained allowed us to affirm that it was possible to replace conventional fertilization using chemical products and ensure adequate crop nutrition by supplying the main macronutrients.

The effect of phosphate mining activities on rhizosphere bacterial communities of surrounding vegetables and crops

The effects of phosphate mining on rhizosphere bacteria in surrounding vegetables and crops, including Lactuca sativa, Glycine max, and Triticum aestivum, are assessed in this study. As results, phosphate mining significantly increased the contents of some large elements, trace elements, and heavy metals in the surrounding agricultural soil, including phosphorus, magnesium, boron, cadmium, lead, arsenic, zinc, and chromium (P < 0.05). The community richness and diversity of bacteria in rhizosphere of the three crops were significantly reduced by phosphate mining (P < 0.05). Abundances of Sphingomonas and RB41 in the rhizosphere soil of phosphate mining area improved compared with the baseline in the non-phosphate mining area. Beta diversity analysis indicated that phosphate mining led to the differentiation of bacterial community structure in plant rhizospheres. Bacterial metabolic analysis indicated that different plant rhizosphere microbial flora developed various metabolic strategies in response to phosphate mining stress, including enriching unsaturated fatty acids, antibiological transport systems, cold shock proteins, etc. This study reveals the interaction between crops, rhizosphere bacteria, and soil pollutants. Select differentiated microbial strains suitable for specific plant rhizosphere environments are necessary for agricultural soil remediation. Additionally, the problem of destruction of agricultural soil and microecology caused by phosphate mining must be solved.

Deciphering the Potential Role of Symbiotic Plant Microbiome and Amino Acid Application on Growth Performance of Chickpea Under Field Conditions

The unprecedented rise in the human population has increased pressure on agriculture production. To enhance the production of crops, farmers mainly rely on the use of chemical fertilizers and pesticides, which have, undoubtedly, increased the production rate but at the cost of losing sustainability of the environment in the form of genetic erosion of indigenous varieties of crops and loss of fertile land. Therefore, farming practices need to upgrade toward the use of biological agents to maintain the sustainability of agriculture and the environment. In this context, using microbial inoculants and amino acids may present a more effective, safer, economical, and sustainable alternative means of realizing higher productivity of crops. Therefore, field experiments were performed on chickpea for two succeeding years using Rhizobium and L-methionine (at three levels, i.e., 5, 10, and 15 mg L-1) separately and in combinations. The results show that the application of Rhizobium and all the three levels of L-methionine increased the growth and yield of chickpea. There was a higher response to a lower dose of L-methionine, i.e., 5 mg L-1. It has been found that maximum grain yield (39.96 and 34.5% in the first and second years, respectively) of chickpea was obtained with the combined use of Rhizobium and L-methionine (5 mg L-1). This treatment was also the most effective in enhancing nodule number (91.6 and 58.19%), leghemoglobin (161.1 and 131.3%), and protein content (45.2 and 45%) of plants in both years. Likewise, photosynthetic pigments and seed chemical composition were significantly improved by Rhizobium inoculation. However, these effects were prominent when Rhizobium inoculation was accompanied by L-methionine. In conclusion, utilizing the potential of combined use of L-methionine and microbial inoculant could be a better approach for developing sustainable agriculture production.