Microbiological Insights into the Stress-Alleviating Property of an Endophytic Bacillus altitudinis WR10 in Wheat under Low-Phosphorus and High-Salinity Stresses

The legacy of endophytes for the formation of bioactive agents, pigments, biofertilizers, nanoparticles and bioremediation of environment

Endophytes have significant prospects for applications beyond their existing utilization in agriculture and the natural sciences. They form an endosymbiotic relationship with plants by colonizing the root tissues without detrimental effects. These endophytes comprise several microorganisms, including bacteria and fungi. They act as repositories of compounds of medicinal importance. They are considered sources of pigments besides synthetic dyes and assist with soil fertility and plant growth as bio-fertilizers. They also have immense potential for advanced technology using endophyte-synthesized nanoparticles. In assisting bioremediation, they facilitate detoxification of pollutants in all spheres of the environment. Studies on the potential of endophytic microbes in drug discovery and biotic stress management are underway. In this review, published databases on endophytes and their diverse roles and applications in various fields, such as bio-fertilizers and nanoparticles, as well as bioremediation, are critically discussed while exploring unanswered questions. In addition, future perspectives on endosymbiotic microorganisms and their prospective use in plants, environmental management, and medicine are discussed in this review.

Global Insights into the Lysine Acetylome Reveal the Role of Lysine Acetylation in the Adaptation of Bacillus altitudinis to Salt Stress

Bacillus altitudinis is a well-known beneficial microorganism in plant rhizosphere, capable of enhancing plant growth and salt tolerance in saline soils. However, the mechanistic changes underlying salt tolerance in B. altitudinis at the level of post-translational modifications remain unclear. Here, diverse lysine modifications including acetylation, succinylation, crotonylation, and malonylation were determined in the B. altitudinis response to salt stress by immunodetection, and the acetylation level greatly increased under salt stress. The in-depth acetylome landscape showed that 1032 proteins in B. altitudinis were differentially acetylated under salt stress. These proteins were involved in many physiological aspects closely related to salt tolerance like energy generation and conversion, amino acid synthesis and transport, cell motility, signal transduction, secretion system, and repair system. Moreover, we also identified the differential acetylation of key enzymes involved in the major osmolyte biosynthesis and conversion and antioxidant defenses. Thiol peroxidase (TPX), a key protective antioxidant enzyme, had 3 upregulated acetylation sites (K7/139/157) under salt stress. Site-specific mutations demonstrated that K7/139/157 acetylation strongly regulated TPX function in scavenging intracellular ROS, thereby impacting bacterial growth under salt stress. To our knowledge, this is the first study showing that bacteria adaptation to salt stress occurs at the level of PTMs.

Recent advances in unraveling the mystery of combined nutrient stress in plants

Efficiently regulating growth to adapt to varying resource availability is crucial for organisms, including plants. In particular, the acquisition of essential nutrients is vital for plant development, as a shortage of just one nutrient can significantly decrease crop yield. However, plants constantly experience fluctuations in the presence of multiple essential mineral nutrients, leading to combined nutrient stress conditions. Unfortunately, our understanding of how plants perceive and respond to these multiple stresses remains limited. Unlocking this mystery could provide valuable insights and help enhance plant nutrition strategies. This review focuses specifically on the regulation of phosphorous homeostasis in plants, with a primary emphasis on recent studies that have shed light on the intricate interactions between phosphorous and other essential elements, such as nitrogen, iron, and zinc, as well as non-essential elements like aluminum and sodium. By summarizing and consolidating these findings, this review aims to contribute to a better understanding of how plants respond to and cope with combined nutrient stress.

Biofilms formation in plant growth-promoting bacteria for alleviating agro-environmental stress

Biofilm formation represents a pivotal and adaptable trait among microorganisms within natural environments. This attribute plays a multifaceted role across diverse contexts, including environmental, aquatic, industrial, and medical systems. While previous research has primarily focused on the adverse impacts of biofilms, harnessing their potential effectively could confer substantial advantages to humanity. In the face of escalating environmental pressures (e.g., drought, salinity, extreme temperatures, and heavy metal pollution), which jeopardize global crop yields, enhancing crop stress tolerance becomes a paramount endeavor for restoring sufficient food production. Recently, biofilm-forming plant growth-promoting bacteria (PGPB) have emerged as promising candidates for agricultural application. These biofilms are evidence of microorganism colonization on plant roots. Their remarkable stress resilience empowers crops to thrive and yield even in harsh conditions. This is accomplished through increased root colonization, improved soil properties, and the synthesis of valuable secondary metabolites (e.g., ACC deaminase, acetin, 2,3-butanediol, proline, etc.). This article elucidates the mechanisms underpinning the role of biofilm-forming PGPB in bolstering plant growth amidst environmental challenges. Furthermore, it explores the tangible applications of these biofilms in agriculture and delves into strategies for manipulating biofilm formation to extract maximal benefits in practical crop production scenarios.

Aspergillus niger Fermentation Broth Promotes Maize Germination and Alleviates Low Phosphorus Stress

Aspergillus niger is a type of soil fungus with the ability to dissolve insoluble phosphate and secrete organic metabolites such as citric acid. However, whether cell-free Aspergillus niger fermentation broth (AFB) promotes maize growth and alleviates low-phosphorus stress has not been reported. In this study, we explored their relationship through a hydroponics system. The results indicated that either too low or too high concentrations of AFB may inhibit seed germination potential and germination rate. Under low phosphorus conditions, all physiological indexes (biomass, soluble sugar content, root length, etc.) increased after AFB was applied. A qRT-PCR analysis revealed that the expression of the EXPB4 and KRP1 genes, which are involved in root development, was upregulated, while the expression of the CAT2 and SOD9 genes, which are keys to the synthesis of antioxidant enzymes, was downregulated. The expression of LOX3, a key gene in lipid peroxidation, was down-regulated, consistent with changes in the corresponding enzyme activity. These results indicate that the application of AFB may alleviate the oxidative stress in maize seedlings, reduce the oxidative damage caused by low P stress, and enhance the resistance to low P stress in maize seedlings. In addition, it reveals the potential of A. niger to promote growth and provides new avenues for research on beneficial plant-fungal interactions.

Transcriptomics and metabolomics revealed that phosphate improves the cold tolerance of alfalfa

INTRODUCTION

Alfalfa (Medicago sativa L.) is a highly nutritious leguminous forage that plays an essential role in animal husbandry. In the middle and high latitudes of the northern hemisphere, there are problems with its low rates of overwintering and production. The application of phosphate (P) is an important measure to improve the cold resistance and production of alfalfa, but little is known about the mechanism of P in improving the cold resistance of alfalfa.

METHODS

This study integrated the transcriptome and metabolome to explain the mechanism of alfalfa in response to low-temperature stress under two applications of P (50 and 200 mg kg^-1) and a control of none applied.

RESULTS

The application of P fertilizer improved the root structure and increased the content of soluble sugar and soluble protein in the root crown. In addition, there were 49 differentially expressed genes (DEGs) with 23 upregulated and 24 metabolites with 12 upregulated when 50 mg kg^-1 of P was applied. In contrast, there were 224 DEGs with 173 upregulated and 12 metabolites with 6 upregulated in the plants treated with 200 mg kg^-1 of P compared with the Control Check (CK). These genes and metabolites were significantly enriched in the biosynthesis of other secondary metabolites and the metabolic pathways of carbohydrates and amino acids. The integration of the transcriptome and metabolome indicated that P affected the biosynthesis of N-acetyl-L-phenylalanine, L-serine, lactose, and isocitrate during the period of increasing cold. It could also affect the expression of related genes that regulate cold tolerance in alfalfa.

DISCUSSION

Our findings could contribute to a deeper understanding of the mechanism that alfalfa uses to tolerate cold and lay a theoretical foundation for breeding alfalfa that is highly efficient at utilizing phosphorus.

Harnessing Native Bacillus spp. for Sustainable Wheat Production

The genus Bacillus has been widely applied in contemporary agriculture as an environmentally-friendly biological agent. However, the real effect of commercial Bacillus-based fertilizers and pesticides varies immensely in the field. To harness Bacillus for efficient wheat production, we reviewed the diversity, functionality, and applicability of wheat-associated native Bacillus for the first time. Our main findings are: (i) Bacillus spp. inhabit the rhizosphere, root, stem, leaf, and kernel of wheat; (ii) B. subtilis and B. velezensis are the most widely endophytic species that can be isolated from both below and aboveground tissues; (iii) major functions of these representative strains are promotion of plant growth and alleviation of both abiotic and biotic stresses in wheat; (iv) stability and effectiveness are 2 major challenges during field application; (v) a STVAE pipeline that includes 5 processes, namely, Screen, Test, Validation, Application, and Evaluation, has been proposed for the capture and refinement of wheat-associated Bacillus spp. In particular, this review comprehensively addresses possible solutions, concerns, and criteria during the development of native Bacillus-based inoculants for sustainable wheat production.

Biocontrol potential and action mechanism of Bacillus amyloliquefaciens DB2 on Bipolaris sorokiniana

Introduction

Bipolaris sorokiniana is the popular pathogenic fungi fungus which lead to common root rot and leaf spot on wheat. Generally, chemical fungicides are used to control diseases. However, the environmental pollution resulting from fungicides should not be ignored. It is important to study the mode of antagonistic action between biocontrol microbes and plant pathogens to design efficient biocontrol strategies.

Results

An antagonistic bacterium DB2 was isolated and identified as Bacillus amyloliquefaciens. The inhibition rate of cell-free culture filtrate (CF, 20%, v/v) of DB2 against B. sorokiniana reached 92.67%. Light microscopy and scanning electron microscopy (SEM) showed that the CF significantly altered the mycelial morphology of B. sorokiniana and disrupted cellular integrity. Fluorescence microscopy showed that culture filtrate destroyed mycelial cell membrane integrity, decreased the mitochondrial transmembrane potential, induced reactive oxygen species (ROS) accumulation, and nuclear damage which caused cell death in B. sorokiniana. Moreover, the strain exhibited considerable production of protease and amylase, and showed a significant siderophore and indole-3-acetic acid (IAA) production. In the detached leaves and potted plants control assay, B. amyloliquefacien DB2 had remarkable inhibition activity against B. sorokiniana and the pot control efficacy was 75.22%. Furthermore, DB2 suspension had a significant promotion for wheat seedlings growth.

Conclusion

B. amyloliquefaciens DB2 can be taken as a potential biocontrol agent to inhibit B. sorokiniana on wheat and promote wheat growth.

Isolation and identification of plant growth-promoting rhizobacteria from tall fescue rhizosphere and their functions under salt stress

Soil salinity has become one of the major factors that threaten tall fescue growth and turf quality. Plants recruit diverse microorganisms in the rhizosphere to cope with salinity stress. In this study, 15 plant growth-promoting rhizobacteria (PGPR) were isolated from the salt-treated rhizosphere of tall fescue and were annotated to 10 genera, including Agrobacterium, Fictibacillus, Rhizobium, Bhargavaea, Microbacterium, Paenarthrobacter, Pseudarthrobacter, Bacillus, Halomonas, and Paracoccus. All strains could produce indole-3-acetic acid (IAA). Additionally, eight strains exhibited the ability to solubilize phosphate and potassium. Most strains could grow on the medium containing 600 mM NaCl, such as Bacillus zanthoxyli and Bacillus altitudinis. Furthermore, Bacillus zanthoxyli and Bacillus altitudinis were inoculated with tall fescue seeds and seedlings to determine their growth-promoting effect. The results showed that Bacillus altitudinis and mixed culture significantly increased the germination rate of tall fescue seeds. Bacillus zanthoxyli can significantly increase the tillers number and leaf width of seedlings under salt conditions. Through the synergistic effect of FaSOS1, FaHKT1, and FaHAK1 genes, Bacillus zanthoxyli helps to expel the excess Na⁺ from aboveground parts and absorb more K⁺ in roots to maintain ion homeostasis in tall fescue. Unexpectedly, we found that Bacillus altitudinis displayed an inapparent growth-promoting effect on seedlings under salt stress. Interestingly, the mixed culture of the two strains was also able to alleviate, to some extent, the effects of salt stress on tall fescue. This study provides a preliminary understanding of tall fescue rhizobacteria and highlights the role of Bacillus zanthoxyli in tall fescue growth and salt tolerance.

Halotolerant Bacillus altitudinis WR10 improves salt tolerance in wheat via a multi-level mechanism

Soil salinity is an important abiotic stress factor that seriously affects the crop growth and yield. Use of plant-derived microorganisms is a promising strategy to alleviate salt stress. In a previous study, the endophytic strain Bacillus altitudinis WR10 isolated from wheat roots showed high salt resistance. In this study, we investigated the efficacy of WR10 in improving the salt tolerance of wheat and its potential mechanisms using a hydroponic test. Under salt stress, WR10 inoculation significantly increased the lengths and dry weights of the roots and shoots, indicating that WR10 improves wheat salt tolerance at the seedling stage. WR10 inoculation significantly reduced Na⁺ accumulation and enhanced K⁺, P, and Ca²⁺ uptake in salt-stressed plants, which can be attributed to the upregulated gene expression of H⁺-ATPase as well as the P-solubilizing and biofilm-producing characteristics of WR10. At the transcriptional level, L-ascorbate peroxidase (APX), glutathione (GSH) synthetase related to GSH biosynthesis, and phenylpropanoid biosynthesis genes (CYP73A, 4CL, and CAD) were significantly upregulated, whereas those of GSH metabolism genes (glutathione S-transferase and gamma-glutamyltranspeptidase) were significantly downregulated in WR10-applied wheat roots under salt stress. These changes increased the APX activity and GSH levels and resulted in a decrease in hydrogen peroxide levels. Additionally, a decrease in proline content was observed in WR10-inoculated plants under salt stress because of WR10-induced upregulation of proline dehydrogenase gene expression. These results provide supporting evidence that WR10 improves wheat salt tolerance via more than one mechanism and open a window of opportunity for WR10 application in salinized soil.

Isolation and Genome Sequence of a Novel Phosphate-Solubilizing Rhizobacterium Bacillus altitudinis GQYP101 and Its Effects on Rhizosphere Microbial Community Structure and Functional Traits of Corn Seedling

Bacillus altitudinis is a widely distributed soil bacterium that has various functional activities, including remediation of contaminated soil, degradation of herbicides, and enhancement of plant growth. B. altitudinis GQYP101 was isolated from the rhizosphere soil of Lycium barbarum L. and demonstrated potential as a plant growth-promoting bacterium. In this work, strain GQYP101 could solubilize phosphorus, and increased the stem diameter, maximum leaf area, and fresh weight of corn in a pot experiment. Nitrogen and phosphorus contents of corn seedlings (aerial part) increased by 100% and 47.9%, respectively, after application of strain GQYP101. Concurrently, nitrogen and phosphorus contents of corn root also increased, by 55.40% and 20.3%, respectively. Furthermore, rhizosphere soil nutrients were altered and the content of available phosphorus increased by 73.2% after application of strain GQYP101. The mechanism by which strain GQYP101 improved plant growth was further investigated by whole genome sequence analysis. Strain GQYP101 comprises a circular chromosome and a linear plasmid. Some key genes of strain GQYP101 were identified that were related to phosphate solubilization, alkaline phosphatase, chemotaxis, and motility. The findings of this study may provide a theoretical basis for strain GQYP101 to enhance crop yield as microbial fertilizer.

Functional Genetic Diversity and Plant Growth Promoting Potential of Polyphosphate Accumulating Bacteria in Soil

Polyphosphate (polyP) accumulation is an important trait of microorganisms. Implication of polyP accumulating bacteria (PAB) in enhanced biological phosphate removal, heavy metal sequestration, and dissolution of dental enamel is well studied. Phosphorous (P) accumulated within microbial biomass also regulates labile P in soil; however, abundance and diversity of the PAB in soil is still unexplored. Present study investigated the genetic and functional diversity of PAB in rhizosphere soil. Here, we report the abundance of Pseudomonas spp. as high PAB in soil, suggesting their contribution to global P cycling. Additional subset analysis of functional genes i.e., polyphosphate kinase (ppk) and exopolyphosphatase (ppx) in all PAB, indicates their significance in bacterial growth and metabolism. Distribution of functional genes in phylogenetic tree represent a more biologically realistic discrimination for the two genes. Distribution of ppx gene disclosed its phylogenetic conservation at species level, however, clustering of ppk gene of similar species in different clades illustrated its environmental condition mediated modifications. Selected PAB showed tolerance to abiotic stress and strong correlation with plant growth promotary (PGP) traits viz. phosphate solubilization, auxin and siderophore production. Interaction of PAB with A. thaliana enhanced the growth and phosphate status of the plant under salinity stress, suggestive of their importance in P cycling and stress alleviation.

IMPORTANCE Study discovered the abundance of Pseudomonas genera as a high phosphate accumulator in soil. The presence of functional genes (polyphosphate kinase [ppk] and exopolyphosphatase [ppx]) in all PAB depicts their importance in polyphosphate metabolism in bacteria. Genetic and functional diversity reveals conservation of the ppx gene at species level. Furthermore, we found a positive correlation between PAB and plant growth promotary traits, stress tolerance, and salinity stress alleviation in A. thaliana.

Microbial-Assisted Wheat Iron Biofortification Using Endophytic Bacillus altitudinis WR10

Microbial-assisted biofortification attracted much attention recently due to its sustainable and eco-friendly nature for improving nutrient content in wheat. An endophytic strain Bacillus altitudinis WR10, which showed sophistical regulation of iron (Fe) homeostasis in wheat seedlings, inspired us to test its potential for enhancing Fe biofortification in wheat grain. In this study, assays in vitro indicated that WR10 has versatile plant growth-promoting (PGP) traits and bioinformatic analysis predicted its non-pathogenicity. Two inoculation methods, namely, seed soaking and soil spraying, with 10⁷ cfu/ml WR10 cells were applied once before sowing of wheat (Triticum aestivum L. cv. Zhoumai 36) in the field. After wheat maturation, evaluation of yield and nutrients showed a significant increase in the mean number of kernels per spike (KPS) and the content of total nitrogen (N), potassium (K), and Fe in grains. At the grain filling stage, the abundance of Bacillus spp. and the content of N, K, and Fe in the root, the stem, and the leaf were also increased in nearly all tissues, except Fe in the stem and the leaf. Further correlation analysis revealed a positive relationship between the total abundance of Bacillus spp. and the content of N, K, and Fe in grains. Seed staining confirmed the enhanced accumulation of Fe, especially in the embryo and the endosperm. Finally, using a hydroponic coculture model, qPCR quantification indicated effective colonization, internalization, translocation, and replication of strain WR10 in wheat within 48 h. Collectively, strain WR10 assisted successful Fe biofortification in wheat in the field, laying a foundation for further large-scale investigation of its applicability and effectiveness.

Complete Genome Sequence of Bacillus sp. strain WR11, an Endophyte Isolated from Wheat Root Providing Genomic Insights into Its Plant Growth-Promoting Effects

Bacillus sp. strain WR11 isolated from the root of wheat (Triticum aestivum L.) possesses abiotic stress alleviating properties and produces several types of enzymes. However, its genomic information is lacking. The study described the complete genome sequence of the bacterium. The size of the genome was 4 202 080 base pairs that consisted of 4 405 genes in total. The G+C content of the circular genome was 43.53% and there were 4 170 coding genes, 114 pseudo genes, 30 ribosome RNAs, 86 tRNAs, and 5 ncRNAs, based on the Prokaryotic Genome Annotation Pipeline (PGAP). Many genes were related to the stress-alleviating properties and 124 genes existed in the CAZy database. The complete genome data of strain WR11 will provide valuable resources for genetic dissection of its plant growth-promoting function and symbiotic interaction with plant.