Accelerated Growth Rate and Increased Drought Stress Resilience of the Model Grass Brachypodium distachyon Colonized by Bacillus subtilis B26

The role of endophytic salt-tolerant Franconibacter Sp. YSD YN2 in Cyperus esculentus L. Var sativus: impacts on plant growth and mechanisms of salt tolerance

BACKGROUND CYPERUS ESCULENTUS

L. var. sativus (chufa) is a perennial plant known for its nutrient-rich underground tubers and aboveground leaves, which offer significant food and health advantages worldwide. Despite its benefits, salt stress hinders plant growth, thus limiting both yield and quality. While the positive effects of plant growth-promoting endophytes (PGPEs) on plant growth have been established, their particular influence on chufa under salt stress has yet to be investigated. This research focused on examining the principal physiological and metabolic responses of chufa following inoculation with the PGPE Franconibacter sp. YSD YN2 at varying NaCl concentrations.

RESULTS

YSD YN2 exhibited significant salt resistance, robust colonization of plant compartments, and various characteristics (indole-3-acetic acid (IAA) (0.90-14.74 µg/mL), phosphate (P) (0.00-20.00 µg/mL), potassium (K) solubility (1.00-2.50), and exopolysaccharides (EPSs) (0.80-28.09 mg/mL)) under different NaCl concentrations, underscoring its capacity to enhance plant development and recuperation under salt stress. YSD YN2 inoculation significantly enhanced plant growth across different NaCl concentrations, including improvements in shoot height (13.33-26.67%), shoot weight (48.91-115.38%), root length (7.84-13.17%), root weight (39.43-63.06%), relative water content (1.78-10.80%), and the number of tillers (50.00-183.50%). Inoculation with YSD YN2 resulted in increased total chlorophyll contents (25.30-83.57%), improved efficiency of antioxidant enzymes such as peroxidase (POD) (13.81-35.48 fold), superoxide dismutase (SOD) (10.67-13.34%), and catalase (CAT) (25.00-78.95%), diminished malondialdehyde (MDA) accumulation (14.10-31.19%), and increased proline accumulation (11.37-19.64%) in chufa. Additionally, inoculation with YSD YN2 led to a reduction in internal Na+ accumulation and an increase in K+ and Ca2+ absorption.

CONCLUSION

YSD YN2 may serve as a valuable PGPE for improving plant development, photosynthetic pigmentation, oxidative processes, and osmotic control substances, controlling ion absorption, and reducing the harmful impacts of high-salinity chufa.

Resolution of MALDI-TOF compared to whole genome sequencing for identification of Bacillus species isolated from cleanrooms at NASA Johnson Space Center

Introduction

Bacteria are frequently isolated from surfaces in cleanrooms, where astromaterials are curated, at NASA's Lyndon B. Johnson Space Center (JSC). Bacillus species are of particular interest because endospores can endure extreme conditions. Current monitoring programs at JSC rely on culturing microbes from swabs of surfaces followed by identification by 16S rRNA sequencing and the VITEK 2 Compact bacterial identification system. These methods have limited power to resolve Bacillus species. Whole genome sequencing (WGS) is the current standard for bacterial identification but is expensive and time-consuming. Matrix-assisted laser desorption - time of flight mass spectrometry (MALDI-TOF MS), provides a rapid, low-cost, method of identifying bacterial isolates and has a higher resolution than 16S rRNA sequencing, particularly for Bacillus species; however, few studies have compared this method to WGS for identification of Bacillus species isolated from cleanrooms.

Methods

To address this, we selected 15 isolates for analysis with WGS and MALDI-TOF MS. Hybrid next-generation (Illumina) and 3rd-generation (nanopore) sequencing were used to draft genomes. Mass spectra, generated with MALDI-TOF MS, were processed with custom scripts to identify clusters of closely related isolates.

Results

MALDI-TOF MS and WGS identified 13/15 and 9/14 at the species level, respectively, and clusters of species generated from MALDI-TOF MS showed good agreement, in terms of congruence of partitioning, with phylotypes generated with WGS. Pairs of strains that were > 94% similar to each other, in terms of average amino acid identity (AAI) predicted by WGS, consistently showed cosine similarities of mass spectra >0.8. The only discordance was for a pair of isolates that were classified as Paenibacillus species. This pair showed relatively high similarity (0.85) in terms of MALDI-TOF MS but only 85% similarity in terms of AAI. In addition, some strains isolated from cleanrooms at the JSC appeared closely related to strains isolated from spacecraft assembly cleanrooms.

Discussion

Since MALDI-TOF MS costs less than whole genome sequencing and offers a throughput of hundreds of isolates per hour, this approach appears to offer a cost-efficient option for identifying Bacillus species, and related microbes, isolated during routine monitoring of cleanrooms and similar built environments.

Effects of Enterobacter cloacae extract, selenium nanoparticles and methyl jasmonate on shoot liquid cultures of Sarcocornia fruticosa under salinity stress

BACKGROUND

The in vitro propagation of halophytes is innovative perspective for sustainable agriculture, conservation of natural plants and essential raw materials for industry due to increasing soil salinization and decreasing freshwater availability. Sarcocornia fruticosa, a halophytic plant, may hold promise for biosaline production systems and achieve bioactive products. Understanding the salt tolerance mechanisms of halophytes through elicitors can enhance the production of secondary metabolites, such as phenolics and flavonoids, under saline environment. This study aimed to evaluate the effects of NaCl salinity (700 mM and 1000 mM) on Sarcocornia fruticosa shoot cultures and assess the influence of different elicitors-Enterobacter cloacae extract (BE), selenium nanoparticles (SeNPs) and methyl jasmonate (MeJA) -on the plants growth, physiological and biochemical responses, and isorhamnetin production.

METHODOLOGY

Shoot cultures were grown under controlled conditions with two concentrations of NaCl, alone and in combination with BE (0.5%), SeNPs (100 ppm), or MeJA (50 µM). Growth parameters, photosynthetic pigments, ion accumulation, osmolyte content, oxidative stress marker, enzyme activity, phenolic compound levels, and isorhamnetin production were analyzed to determine the impact of salinity and elicitor treatments on S. fruticosa for 14 days.

RESULTS

Sarcorcocnia fruticosa exhibited better tolerance up to 700 mM than 1000 mM NaCl, as evidenced by higher dry weights, chlorophyll a/b ratios, and enhanced osmolyte and antioxidant contents. Elicitation both saline cultures with BE and SeNPs improved growth mostly by increasing biomass, pigment contents, K+/Na+ ratios, and reducing lipid peroxidation, however, MeJA reduced the biomass mainly by increasing MDA and Na+ ion accumulation. In contrast, application of all elicitors stimulated the production of phenolic compounds and isorhamnetin, as well as BE can contribute for increasing resistance of S. fruticosa to stressful conditions.

CONCLUSION

This study demonstrated that PTC techniques and appropriate elicitors can optimize halophyte propagation and secondary metabolite production under saline conditions. The findings suggest that BE and SeNPs significantly enhanced the growth and biochemical resilience of S. fruticosa under salinity stress, with a notable increase in isorhamnetin production. MEJA.

Impact of water stress to plant epigenetic mechanisms in stress and adaptation

Water is the basic molecule in living beings, and it has a major impact on vital processes. Plants are sessile organisms with a sophisticated regulatory network that regulates how resources are distributed between developmental and adaptation processes. Drought-stressed plants can change their survival strategies to adapt to this unfavorable situation. Indeed, plants modify, change, and modulate gene expression when grown in a low-water environment. This adaptation occurs through several mechanisms that affect the expression of genes, allowing these plants to resist in dry regions. Epigenetic modulation has emerged as a major factor in the transcription regulation of drought stress-related genes. Moreover, specific molecular and epigenetic modifications in the expression of certain genetic networks lead to adapted responses that aid a plant's acclimatization and survival during repeated stress. Indeed, understanding plant responses to severe environmental stresses, including drought, is critical for biotechnological applications. Here, we first focused on drought stress in plants and their general adaptation mechanisms to this stress. We also discussed plant epigenetic regulation when exposed to water stress and how this adaptation can be passed down through generations.

Rhizobacteria and Phytohormonal interactions increase Drought Tolerance in Phaseolus vulgaris through enhanced physiological and biochemical efficiency

The cultivation of common beans (Phaseolus vulgaris L.) in semi-arid regions is affected by drought. To explore potential alleviation strategies, we investigated the impact of inoculation with Bacillus velezensis, and the application of acetylsalicylic acid (ASA) via foliage application (FA), which promote plant growth and enhance stress tolerance. A split-split-plot experiment with four replications was conducted, featuring two irrigation levels: full watering (FW, 100% of plant water requirements) and deficit watering (DW, 70% of plant water requirements) as a main plot, two ASA levels (No foliage application (NFA) 0 and 0.5 mM) as sub plot, and bacterial inoculation (BI) versus non-bacterial inoculation (NBI) as sub-sub plot. Results showed that the highest grain yield was achieved with the ASA + BI under FW (3270 kg ha-¹), a 56% increase compared to the control (2094 kg ha-¹). Under DW, the ASA + BI increased yield by approximately 30%. ASA significantly increased relative water content under deficit watering, achieving 84% with BI. Chlorophyll a content peaked at 3.11 mg g- 1 with full watering, and chlorophyll b content increased by up to 23.8% under deficit watering, indicating improved photosynthetic capacity. Malondialdehyde and hydrogen peroxide levels were reduced to 10.88 and 14.81 µmol g-¹ fresh weight, respectively, in ASA + BI treatments, demonstrating reduced oxidative stress. Antioxidant enzyme activities were significantly elevated in treated plants under DW. This study demonstrates the potential of microbial and hormonal treatments in boosting drought tolerance in common beans, providing a viable approach for sustaining crop performance under stress conditions.

Identification of DEMETER-like DNA demethylase gene family in citrus and their role in drought stress-adaptive responses

DEMETER-Like DNA demethylases (DMLs) are epigenetic regulators of many developmental and biological processes in plants. No comprehensive information about the DML gene family in citrus is available to date. Here, a total of three DML genes in the genomes of Citrus sinensis (named CsDML1-3) and C. clementina (named CcDML1-3) were identified and analyzed. They encode hydrophilic and relatively large proteins, with prediction of nuclear localization, containing the conserved domains and motifs typical of plant DMLs. Protein interaction network analysis suggested that they interact primarily with proteins related to the maintenance of DNA methylation and remodeling of chromatin. Analysis of their promoter regions led to the identification of several cis-acting regulatory elements involved in stress response, including drought, heat and cold stresses. The presence of several miRNA targets and potential phosphorylation sites suggest that their expression is also regulated at post-transcriptional and post-translational levels. RNA-Seq data and quantitative real-time PCR analysis showed a low and drought-regulated gene expression of the citrus DMLs in different plant tissues. CsDML1 and CsDML3 were also differentially regulated by deficit irrigation in fruits at different developmental stages, with a positive and significant correlation found between CsDML1 and PHYTOENE SYNTHASE (PSY) and between CsDML3 and ATP CITRATE LYASEs (ACLs) and ZETA-CAROTENE DESATURASE (ZDS) gene expression. These results indicate that the citrus DMLs are potentially functional enzymes involved in developmental processes and drought stress-adaptive responses, providing a useful reference for further investigation of their functions and applications on the citrus improvement.

The Influence of Chitosan Derivatives in Combination with Bacillus subtilis Bacteria on the Development of Systemic Resistance in Potato Plants with Viral Infection and Drought

Viral diseases of potatoes are among the main problems causing deterioration in the quality of tubers and loss of yield. The growth and development of potato plants largely depend on soil moisture. Prevention strategies require comprehensive protection against pathogens and abiotic stresses, including modeling the beneficial microbiome of agroecosystems combining microorganisms and immunostimulants. Chitosan and its derivatives have great potential for use in agricultural engineering due to their ability to induce plant immune responses. The effect of chitosan conjugate with caffeic acid (ChCA) in combination with Bacillus subtilis 47 on the transcriptional activity of PR protein genes and changes in the proteome of potato plants during potato virus Y (PVY) infection and drought was studied. The mechanisms of increasing the resistance of potato plants to PVY and lack of moisture are associated with the activation of transcription of genes encoding PR proteins: the main protective protein (PR-1), chitinase (PR-3), thaumatin-like protein (PR-5), protease inhibitor (PR-6), peroxidase (PR-9), and ribonuclease (PR-10), as well as qualitative and quantitative changes in the plant proteome. The revealed activation of the expression of marker genes of systemic acquired resistance and induced systemic resistance under the influence of combined treatment with B. subtilis and chitosan conjugate indicate that, in potato plants, the formation of resistance to viral infection in drought conditions proceeds synergistically. By two-dimensional electrophoresis of S. tuberosum leaf proteins followed by MALDI-TOF analysis, 10 proteins were identified, the content and composition of which differed depending on the experiment variant. In infected plants treated with ChCA, the synthesis of proteinaceous RNase P 1 and oxygen-evolving enhancer protein 2 was enhanced in conditions of normal humidity, and 20 kDa chaperonin and TMV resistance protein N-like was enhanced in conditions of lack of moisture. The virus coat proteins were detected, which intensively accumulated in the leaves of plants infected with potato Y-virus. ChCA treatment reduced the content of these proteins in the leaves, and in plants treated with ChCA in combination with Bacillus subtilis, viral proteins were not detected at all, both in conditions of normal humidity and lack of moisture, which suggests the promising use of chitosan derivatives in combination with B. subtilis bacteria in the regulation of plant resistance.

Natural variation in Brachypodium distachyon responses to combined abiotic stresses

The demand for agricultural production is becoming more challenging as climate change increases global temperature and the frequency of extreme weather events. This study examines the phenotypic variation of 149 accessions of Brachypodium distachyon under drought, heat, and the combination of stresses. Heat alone causes the largest amounts of tissue damage while the combination of stresses causes the largest decrease in biomass compared to other treatments. Notably, Bd21-0, the reference line for B. distachyon, did not have robust growth under stress conditions, especially the heat and combined drought and heat treatments. The climate of origin was significantly associated with B. distachyon responses to the assessed stress conditions. Additionally, a GWAS found loci associated with changes in plant height and the amount of damaged tissue under stress. Some of these SNPs were closely located to genes known to be involved in responses to abiotic stresses and point to potential causative loci in plant stress response. However, SNPs found to be significantly associated with a response to heat or drought individually are not also significantly associated with the combination of stresses. This, with the phenotypic data, suggests that the effects of these abiotic stresses are not simply additive, and the responses to the combined stresses differ from drought and heat alone.

Unveiling the dynamic relationship of viruses and/or symbiotic bacteria with plant resilience in abiotic stress

In the ecosphere, plants interact with environmental biotic and abiotic partners, where unbalanced interactions can induce unfavourable stress conditions. Abiotic factors (temperature, water, and salt) are primarily required for plants healthy survival, and any change in their availability is reflected as a stress signal. In certain cases, the presence of infectious pathogens such as viruses, bacteria, fungi, protozoa, nematodes, and insects can also create stress conditions in plants, leading to the emergence of disease or deficiency symptoms. While these symptoms are often typical of abiotic or biotic stress, however, there are instances where they can intensify under specific conditions. Here, we primarily summarize the viral interactions with plants during abiotic stress to understand how these associations are linked together during viral pathogenesis. Secondly, focus is given to the beneficial effects of root-associated symbiotic bacteria in fulfilling the basic needs of plants during normal as well as abiotic stress conditions. The modulations of plant functional proteins, and their occurrence/cross-talk, with pathogen (virus) and symbiont (bacteria) molecules are also discussed. Furthermore, we have highlighted the biochemical and systematic adaptations that develop in plants due to bacterial symbiosis to encounter stress hallmarks. Lastly, directions are provided towards exploring potential rhizospheric bacteria to maintain plant-microbes ecosystem and manage abiotic stress in plants to achieve better trait health in the horticulture crops.

Meta-analysis of plant growth-promoting rhizobacteria interaction with host plants: implications for drought stress response gene expression

Introduction

The molecular and physiological mechanisms activated in plants during drought stress tolerance are regulated by several key genes with both metabolic and regulatory roles. Studies focusing on crop gene expression following plant growth-promoting rhizobacteria (PGPR) inoculation may help understand which bioinoculant is closely related to the induction of abiotic stress responses.

Methods

Here, we performed a meta-analysis following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines to summarise information regarding plant-PGPR interactions, focusing on the regulation of nine genes involved in plant drought stress response. The literature research yielded 3,338 reports, of which only 41 were included in the meta-analysis based on the chosen inclusion criteria. The meta-analysis was performed on four genes (ACO, APX, ACS and DREB2); the other five genes (ERD15, MYB, MYC, acdS, WRKY) had an insufficient number of eligible articles.

Results

Forest plots obtained through each meta-analysis showed that the overexpression of ACO, APX, ACS and DREB2 genes was not statistically significant. Unlike the other genes, DREB2 showed statistically significant results in both the presence and absence of PGPR. Considering I2>75 %, the results showed a high heterogeneity among the studies included, and the cause for this was examined using subgroup analysis. Moreover, the funnel plot and Egger's test showed that the analyses were affected by strong publication bias.

Discussion

This study argues that the presence of PGPR may not significantly influence the expression of drought stress response-related crop genes. This finding may be due to high heterogeneity, lack of data on the genes examined, and significant publication bias.

Vertical transfer and functional characterization of cotton seed core microbiome

Introduction

Microbiome within plant tissues is pivotal for co-evolution with host plants. This microbiome can colonize the plant, with potential transmission via seeds between parents and offspring, affecting seedling growth and host plant adaptability to the environment.

Methods

We employed 16S rRNA gene amplicon analysis to investigate the vertical distribution of core microbiome in cotton seeds across ecological niches [rhizosphere, root, stem, leaf, seed and seed-P (parental seed)] of the three cotton genotypes.

Results

The findings demonstrated a significant decrease in microbiome diversity and network complexity from roots, stems, and leaves to seeds. The microenvironment exerted a more substantial influence on the microbiome structure of cotton than the genotypes. The core endophytic microorganisms in cotton seeds comprised 29 amplicon sequence variants (ASVs) affiliated with Acidimicrobiia, Alphaproteobacteria, Bacilli, Bacteroidia, Clostridia, Gammaproteobacteria, and unclassified_Proteobacteria. These vertically transmitted taxa are widely distributed in cotton plants. Through 16S rRNA gene-based function prediction analysis of the cotton microbiome, we preliminarily understood that there are potential differences in metabolic capabilities and phenotypic traits among microbiomes in different microhabitats.

Discussion

In conclusion, this study demonstrated the crucial role of the microenvironment in influencing the cotton microbiome and offered insights into the structures and functions of the cotton seed microbiome, facilitating future crop yield enhancement through core seed microbiome regulation.

Epigenetic and Hormonal Modulation in Plant-Plant Growth-Promoting Microorganism Symbiosis for Drought-Resilient Agriculture

Plant growth-promoting microorganisms (PGPMs) have emerged as valuable allies for enhancing plant growth, health, and productivity across diverse environmental conditions. However, the complex molecular mechanisms governing plant-PGPM symbiosis under the climatic hazard of drought, which is critically challenging global food security, remain largely unknown. This comprehensive review explores the involved molecular interactions that underpin plant-PGPM partnerships during drought stress, thereby offering insights into hormonal regulation and epigenetic modulation. This review explores the challenges and prospects associated with optimizing and deploying PGPMs to promote sustainable agriculture in the face of drought stress. In summary, it offers strategic recommendations to propel research efforts and facilitate the practical implementation of PGPMs, thereby enhancing their efficacy in mitigating drought-detrimental effects in agricultural soils.

Current Scenario and Future Prospects of Endophytic Microbes: Promising Candidates for Abiotic and Biotic Stress Management for Agricultural and Environmental Sustainability

Globally, substantial research into endophytic microbes is being conducted to increase agricultural and environmental sustainability. Endophytic microbes such as bacteria, actinomycetes, and fungi inhabit ubiquitously within the tissues of all plant species without causing any harm or disease. Endophytes form symbiotic relationships with diverse plant species and can regulate numerous host functions, including resistance to abiotic and biotic stresses, growth and development, and stimulating immune systems. Moreover, plant endophytes play a dominant role in nutrient cycling, biodegradation, and bioremediation, and are widely used in many industries. Endophytes have a stronger predisposition for enhancing mineral and metal solubility by cells through the secretion of organic acids with low molecular weight and metal-specific ligands (such as siderophores) that alter soil pH and boost binding activity. Finally, endophytes synthesize various bioactive compounds with high competence that are promising candidates for new drugs, antibiotics, and medicines. Bioprospecting of endophytic novel secondary metabolites has given momentum to sustainable agriculture for combating environmental stresses. Biotechnological interventions with the aid of endophytes played a pivotal role in crop improvement to mitigate biotic and abiotic stress conditions like drought, salinity, xenobiotic compounds, and heavy metals. Identification of putative genes from endophytes conferring resistance and tolerance to crop diseases, apart from those involved in the accumulation and degradation of contaminants, could open new avenues in agricultural research and development. Furthermore, a detailed molecular and biochemical understanding of endophyte entry and colonization strategy in the host would better help in manipulating crop productivity under changing climatic conditions. Therefore, the present review highlights current research trends based on the SCOPUS database, potential biotechnological interventions of endophytic microorganisms in combating environmental stresses influencing crop productivity, future opportunities of endophytes in improving plant stress tolerance, and their contribution to sustainable remediation of hazardous environmental contaminants.

Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots

For a deeper and comprehensive understanding of the composition and function of rhizosphere microbiomes, we need to focus at the scale of individual roots in standardized growth containers. Root exudation patterns are known to vary along distinct parts of the root even in juvenile plants giving rise to spatially distinct microbial niches. To address this, we analyzed the microbial community from two spatially distinct zones of the developing primary root (tip and base) in young Brachypodium distachyon grown in natural soil using standardized fabricated ecosystems known as EcoFABs as well as in more conventional pot and tubes. 16S rRNA based community analysis showed a strong rhizosphere effect resulting in significant enrichment of several OTUs belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. However, microbial community composition did not differ between root tips and root base or across different growth containers. Functional analysis of bulk metagenomics revealed significant differences between root tips and bulk soil. The genes associated with different metabolic pathways and root colonization were enriched in root tips. On the other hand, genes associated with nutrient-limitation and environmental stress were prominent in the bulk soil compared to root tips, implying the absence of easily available, labile carbon and nutrients in bulk soil relative to roots. Such insights into the relationships between developing root and microbial communities are critical for judicious understanding of plant-microbe interactions in early developmental stages of plants.

Transcriptional landscape of Brachypodium distachyon roots during interaction with Bacillus velezensis strain B26

Plant growth promoting rhizobacteria (PGPR) communicate with plants through roots. The molecular mechanism by which plants and PGPR respond to each other is not very well known. In the current study, we did RNA sequence analysis of Brachypodium distachyon Bd21-3 roots inoculated with PGPR, Bacillus velezensis strain B26. From our list of differentially expressed genes, we concentrated on transcripts that have a high possibility of participating in plant-PGPR interaction. Transcripts associated to the hormone signalling pathway were differentially expressed. We identified the upregulation of various transcripts linked to ion transporters. Reduction in expression of defense signalling genes indicated that B26 suppresses the plant defense mechanisms to begin successful interaction with roots. Transcripts associated with lignin branch of the phenylpropanoid pathway were upregulated as well, leading to more accumulation of lignin in the cell wall which enhances mechanical strength of plants. Overall, this study is an excellent resource for investigating associations between plant-PGPR interactions.

Watermelon Root Exudates Enhance Root Colonization of Bacillus amyloliquefaciens TR2

Bacillus amyloliquefaciens TR2, one of plant growth-promoting rhizobacteria (PGPR), is capable of colonizing plant roots in a large population size. However, the interaction of watermelon root exudates and colonization of the strain TR2 has not yet been clearly elucidated. In this investigation, we demonstrated that B. amyloliquefaciens TR2 promoted watermelon plants growth and exhibited biocontrol efficacy against watermelon Fusarium wilt under greenhouse conditions. Collected watermelon root exudates significantly induced chemotaxis, swarming motility, and biofilm formation of the strain TR2. We also tested the components of root exudates (organic acids: malic acid, citric acid, succinic acid, and fumaric acid; amino acids: methionine, glutamic acid, alanine, and aspartic acid; phenolic acid: benzoic acid) and the results showed that a majority of these compounds could promote chemotactic response, swarming motility, and biofilm formation in a different degree. Benzoic acid induced the strongest chemotactic response; however, the swarming motility and biofilm formation of the strain TR2 were maximumly enhanced by supplement of fumaric acid and glutamic acid, respectively. In addition, the root colonization examination indicated that the population of B. amyloliquefaciens TR2 colonized on watermelon root surfaces was dramatically increased by adding concentrated watermelon root exudates. In summary, our studies provide evidence suggesting that root exudates are important for colonization of B. amyloliquefaciens TR2 on plant roots and help us to understand the interaction between plants and beneficial bacteria.

Endophytic Pseudomonas sp. from Agave palmeri Participate in the Rhizophagy Cycle and Act as Biostimulants in Crop Plants

Plant growth-promoting bacteria are generating increasing interest in the agricultural industry as a promising alternative to traditional chemical fertilizers; however, much of the focus has been on rhizosphere bacteria. Bacterial endophytes are another promising source of plant growth-promoting bacteria, and though many plants have already been prospected for beneficial microbes, desert plants have been underrepresented in such studies. In this study, we show the growth-promoting potential of five strains of endophytic Pseudomonas sp. isolated from Agave palmeri, an agave from the Sonoran Desert. When inoculated onto Kentucky bluegrass, clover, carrot, coriander, and wheat, endophytic Pseudomonas sp. increased seedling root lengths in all hosts and seedling shoot lengths in Kentucky bluegrass, carrot, and wheat. Transformation of the Pseudomonas sp. strain P3AW to express the fluorescent protein mCherry revealed that Pseudomonas sp. becomes endophytic in non-native hosts and participates in parts of the rhizophagy cycle, a process by which endophytic bacteria cycle between the soil and roots, bringing in nutrients from the soil which are then extracted through reactive oxygen-mediated bacterial degradation in the roots. Tracking of the Pseudomonas sp. strain P3AW also provided evidence for a system of endophyte, or endophyte cell content, transport via the vascular bundle. These results provide further evidence of the rhizophagy cycle in plants and how it relates to growth promotion in plants by biostimulant bacteria.

Bacillus spp. as Bioagents: Uses and Application for Sustainable Agriculture

Food security will be a substantial issue in the near future due to the expeditiously growing global population. The current trend in the agriculture industry entails the extravagant use of synthesized pesticides and fertilizers, making sustainability a difficult challenge. Land degradation, lower production, and vulnerability to both abiotic and biotic stresses are problems caused by the usage of these pesticides and fertilizers. The major goal of sustainable agriculture is to ameliorate productivity and reduce pests and disease prevalence to such a degree that prevents large-scale damage to crops. Agriculture is a composite interrelation among plants, microbes, and soil. Plant microbes play a major role in growth promotion and improve soil fertility as well. Bacillus spp. produces an extensive range of bio-chemicals that assist in plant disease control, promote plant development, and make them suitable for agricultural uses. Bacillus spp. support plant growth by N fixation, P and K solubilization, and phytohormone synthesis, in addition to being the most propitious biocontrol agent. Moreover, Bacilli excrete extracellular metabolites, including antibiotics, lytic enzymes, and siderophores, and demonstrate antagonistic activity against phytopathogens. Bacillus spp. boosts plant resistance toward pathogens by inducing systemic resistance (ISR). The most effective microbial insecticide against insects and pests in agriculture is Bacillus thuringiensis (Bt). Additionally, the incorporation of toxin genes in genetically modified crops increases resistance to insects and pests. There is a constant increase in the identified Bacillus species as potential biocontrol agents. Moreover, they have been involved in the biosynthesis of metallic nanoparticles. The main objective of this review article is to display the uses and application of Bacillus specie as a promising biopesticide in sustainable agriculture. Bacillus spp. strains that are antagonistic and promote plant yield attributes could be valuable in developing novel formulations to lead the way toward sustainable agriculture.

Integrating a Bacillus-based product with fungicides by foliar application to protect soybean: a sustainable approach to avoid exclusive use of chemicals

BACKGROUND

Biological control is widely applied against soybean (Glycine max L.) soil-borne pathogens by furrow or seed treatments. The efficiency of bioproducts and timing of application by foliar sprays against soybean pathogens needs to be more fully understood. This work investigated the efficiency of foliar application with a Bacillus subtilis-based product (BBP) to protect soybean from multiple pathogens and the best moment to apply it considering its compatibility with fungicides.

RESULTS

Foliar applications (from stages V6 to R4) with BBP, mancozeb (M) and systemic fungicides (S) applied against Asian rust (Phakopsora pachyrhizi), BBP followed by S (BBP-S), BBP along with S (S + BBP), S along with M (S + M) or water were carried out in a soybean field for two years. The treatments S + BBP, S + M and BBP-S reduced the severity of Asian rust by 82% compared to the control. Except for M, all treatments reduced the severity of other foliar diseases by >60%. The defoliation was reduced by BBP and BBP-S, whereas the yield was 25% higher than control by using BBP, S + M, S + BBP or BBP-S. Also, the incidence of Fusarium sp. was significantly reduced on seeds from treatments BBP and BBP-S. The compatibility tests in Petri dishes demonstrated that all fungicides decreased the bacterial growth when applied along with BBP, whereas previous applications of BBP did not reduce the bacterial growth.

CONCLUSIONS

The BBP protected soybean against multiple pathogens, reduced defoliation and promoted soybean yield similarly to conventional fungicides, but in general, the early application of the BBP was the most efficient protection. © 2022 Society of Chemical Industry.

Salt Tolerant Bacillus Strains Improve Plant Growth Traits and Regulation of Phytohormones in Wheat under Salinity Stress

Soil salinity is a major constraint adversely affecting agricultural crops including wheat worldwide. The use of plant growth promoting rhizobacteria (PGPR) to alleviate salt stress in crops has attracted the focus of many researchers due to its safe and eco-friendly nature. The current study aimed to study the genetic potential of high halophilic Bacillus strains, isolated from the rhizosphere in the extreme environment of the Qinghai-Tibetan plateau region of China, to reduce salt stress in wheat plants. The genetic analysis of high halophilic strains, NMCN1, LLCG23, and moderate halophilic stain, FZB42, revealed their key genetic features that play an important role in salt stress, osmotic regulation, signal transduction and membrane transport. Consequently, the expression of predicted salt stress-related genes were upregulated in the halophilic strains upon NaCl treatments 10, 16 and 18%, as compared with control. The halophilic strains also induced a stress response in wheat plants through the regulation of lipid peroxidation, abscisic acid and proline in a very efficient manner. Furthermore, NMCN1 and LLCG23 significantly enhanced wheat growth parameters in terms of physiological traits, i.e., fresh weight 31.2% and 29.7%, dry weight 28.6% and 27.3%, shoot length 34.2% and 31.3% and root length 32.4% and 30.2%, respectively, as compared to control plants under high NaCl concentration (200 mmol). The Bacillus strains NMCN1 and LLCG23 efficiently modulated phytohormones, leading to the substantial enhancement of plant tolerance towards salt stress. Therefore, we concluded that NMCN1 and LLCG23 contain a plethora of genetic features enabling them to combat with salt stress, which could be widely used in different bio-formulations to obtain high crop production in saline conditions.

Brachypodium: 20 years as a grass biology model system; the way forward?

It has been 20 years since Brachypodium distachyon was suggested as a model grass species, but ongoing research now encompasses the entire genus. Extensive Brachypodium genome sequencing programmes have provided resources to explore the determinants and drivers of population diversity. This has been accompanied by cytomolecular studies to make Brachypodium a platform to investigate speciation, polyploidisation, perenniality, and various aspects of chromosome and interphase nucleus organisation. The value of Brachypodium as a functional genomic platform has been underscored by the identification of key genes for development, biotic and abiotic stress, and cell wall structure and function. While Brachypodium is relevant to the biofuel industry, its impact goes far beyond that as an intriguing model to study climate change and combinatorial stress.

Glomus sp. and Bacillus sp. strains mitigate the adverse effects of drought on maize (Zea mays L.)

Maize (Zea mays L.) is an economically important source of food and feed. This species is highly sensitive to drought, which is the most limiting factor for the biomass yield of a crop. Thus, maize cultivation methods should be improved, especially by environment-friendly agricultural practices, such as microorganisms. Here, we provide evidence that Glomus sp. and Bacillus sp. modulate maize response to drought. Inoculation of maize seeds by these microorganisms restored the proper photosynthetic activity of the plant under drought and stabilized the osmoprotectant content of the leaf. The beneficial effect of Glomus sp. and Bacillus sp. was also related to the stabilization of cell redox status reflected by hydrogen peroxide content, antioxidant enzymes, and malondialdehyde level in leaves. As we revealed by several methods, shaping maize response to drought is mediated by both microorganism-mediated modifications of cell wall composition and structure of leaves, such as downregulating pectin, affecting their methylation degree, and increasing hemicellulose content. Overall, we provide new information about the mechanisms by which Glomus sp. and Bacillus sp. induce drought tolerance in maize, which is a promising approach for mitigating abiotic stresses.

Is Endophytic Colonization of Host Plants a Method of Alleviating Drought Stress? Conceptualizing the Hidden World of Endophytes

In the wake of changing climatic conditions, plants are frequently exposed to a wide range of biotic and abiotic stresses at various stages of their development, all of which negatively affect their growth, development, and productivity. Drought is one of the most devastating abiotic stresses for most cultivated crops, particularly in arid and semiarid environments. Conventional breeding and biotechnological approaches are used to generate drought-tolerant crop plants. However, these techniques are costly and time-consuming. Plant-colonizing microbes, notably, endophytic fungi, have received increasing attention in recent years since they can boost plant growth and yield and can strengthen plant responses to abiotic stress. In this review, we describe these microorganisms and their relationship with host plants, summarize the current knowledge on how they “reprogram” the plants to promote their growth, productivity, and drought tolerance, and explain why they are promising agents in modern agriculture.

Characterization of plant growth-promoting rhizobacteria (PGPR) in Persian walnut associated with drought stress tolerance

There is a lack of information on the rhizosphere of nut-bearing trees where microbial populations can benefit roots and tree growth. The current research aimed at discovering plant growth-promoting rhizobacteria (PGPR) in the rhizosphere of soil samples from around the root zone of six walnut trees, each of which was considered as a genotype, i.e. 'TT1', 'TT2', 'SS2', 'ZM1', 'Chandler' and 'Haward'. The trees grew in different arid and semiarid regions of Iran and Turkey. The strains were isolated and identified based on different morphological and biochemical markers. Drought-stress tolerance was assessed in the case of each isolate through their transfer to culture medium, containing polyethylene glycol (PEG₆₀₀₀) at 0 and 373.80 g L^-1. Resilient strains were analyzed for measuring their ability to produce siderophore, hydrogen cyanide (HCN), Indole-3-acetic acid (IAA) and Gibberellic acid (GA₃). In sum, 211 isolates were identified, of which a large number belonged to the Bacillus genus and, specifically, 78% of the strains were able to grow under drought stress conditions. The genus Arthrobacter was only detected in the rhizosphere of 'ZM1', 'Haward' and 'TT1' genotypes. In 4% of the strains, IAA production exceeded 53 mg L^-1, while a high level of phosphorus solubility was verified in 6% of the strains. No strain was found to have the capability of producing HCN. The strains were screened for drought-tolerance, which resulted in the discovery of two promising strains, i.e. ZM39 and Cha43. Based on molecular identification through amplification and sequencing of the 16S rDNA gene, these two strains seemed to belong to Bacillus velezensis and Bacillus amyloliquefaciens, respectively. The discovery of new PGPR strains could probably assist walnut trees in improving their mechanisms of adaptation to drought stress.

Plant Development of Early-Maturing Spring Wheat (Triticum aestivum L.) under Inoculation with Bacillus sp. V2026

The effect of a plant growth-promoting bacterium (PGPB) Bacillus sp. V2026, a producer of indolyl-3-acetic acid (IAA) and gibberellic acid (GA), on the ontogenesis and productivity of four genotypes of early-maturing spring wheat was studied under controlled conditions. The inoculation of wheat plants with Bacillus sp. V2026 increased the levels of endogenous IAA and GA in wheat of all genotypes and the level of trans-Zeatin in Sonora 64 and Leningradskaya rannyaya cvs but decreased it in AFI177 and AFI91 ultra-early lines. Interactions between the factors “genotype” and “inoculation” were significant for IAA, GA, and trans-Zeatin concentrations in wheat shoots and roots. The inoculation increased the levels of chlorophylls and carotenoids and reduced lipid peroxidation in leaves of all genotypes. The inoculation resulted in a significant increase in grain yield (by 33–62%), a reduction in the time for passing the stages of ontogenesis (by 2–3 days), and an increase in the content of macro- and microelements and protein in the grain. Early-maturing wheat genotypes showed a different response to inoculation with the bacterium Bacillus sp. V2026. Cv. Leningradskaya rannyaya was most responsive to inoculation with Bacillus sp. V2026.

Molecular mechanisms associated with microbial biostimulant-mediated growth enhancement, priming and drought stress tolerance in maize plants

Microbial-based biostimulants are emerging as effective strategies to improve agricultural productivity; however, the modes of action of such formulations are still largely unknown. Thus, herein we report elucidated metabolic reconfigurations in maize (Zea mays) leaves associated with growth promotion and drought stress tolerance induced by a microbial-based biostimulant, a Bacillus consortium. Morphophysiological measurements revealed that the biostimulant induced a significant increase in biomass and enzymatic regulators of oxidative stress. Furthermore, the targeted metabolomics approach revealed differential quantitative profiles in amino acid-, phytohormone-, flavonoid- and phenolic acid levels in plants treated with the biostimulant under well-watered, mild, and severe drought stress conditions. These metabolic alterations were complemented with gene expression and global DNA methylation profiles. Thus, the postulated framework, describing biostimulant-induced metabolic events in maize plants, provides actionable knowledge necessary for industries and farmers to confidently and innovatively explore, design and fully implement microbial-based formulations and strategies into agronomic practices for sustainable agriculture and food production.

Bacillus velezensis strain B26 modulates the inflorescence and root architecture of Brachypodium distachyon via hormone homeostasis

Plant growth-promoting rhizobacteria (PGPR) influence plant health. However, the genotypic variations in host organisms affect their response to PGPR. To understand the genotypic effect, we screened four diverse B. distachyon genotypes at varying growth stages for their ability to be colonized by B. velezensis strain B26. We reasoned that B26 may have an impact on the phenological growth stages of B. distachyon genotypes. Phenotypic data suggested the role of B26 in increasing the number of awns and root weight in wild type genotypes and overexpressing transgenic lines. Thus, we characterized the expression patterns of flowering pathway genes in inoculated plants and found that strain B26 modulates the transcript abundance of flowering genes. An increased root volume of inoculated plants was estimated by CT-scanning which suggests the role of B26 in altering the root architecture. B26 also modulated plant hormone homeostasis. A differential response was observed in the transcript abundance of auxin and gibberellins biosynthesis genes in inoculated roots. Our results reveal that B. distachyon plant genotype is an essential determinant of whether a PGPR provides benefit or harm to the host and shed new insight into the involvement of B. velezensis in the expression of flowering genes.

Bacillus subtilis Impact on Plant Growth, Soil Health and Environment: Dr. Jekyll and Mr. Hyde

The increased dependence of farmers on chemical fertilizers poses a risk to soil fertility and ecosystem stability. Plant growth-promoting rhizobacteria (PGPR) are at the forefront of sustainable agriculture, providing multiple benefits for the enhancement of crop production and soil health. Bacillus subtilis is a common PGPR in soil that plays a key role in conferring biotic and abiotic stress tolerance to plants by induced systemic resistance (ISR), biofilm formation, and lipopeptide production. As a part of bioremediating technologies, Bacillus spp. can purify metal contaminated soil. It acts as a potent denitrifying agent in agroecosystems while improving the carbon sequestration process when applied in a regulated concentration. Although it harbors several antibiotic resistance genes (ARGs), it can reduce the horizontal transfer of ARGs during manure composting by modifying the genetic makeup of existing microbiota. In some instances, it affects the beneficial microbes of the rhizosphere. External inoculation of B. subtilis has both positive and negative impacts on the endophytic and semi-synthetic microbial community. Soil texture, type, pH, and bacterial concentration play a crucial role in the regulation of all these processes. Soil amendments and microbial consortia of Bacillus produced by microbial engineering could be used to lessen the negative effect on soil microbial diversity. The complex plant-microbe interactions could be decoded using transcriptomics, proteomics, metabolomics, and epigenomics strategies which would be beneficial for both crop productivity and the well-being of soil microbiota. Bacillus subtilis has more positive attributes similar to the character of Dr. Jekyll and some negative attributes on plant growth, soil health, and the environment akin to the character of Mr. Hyde.

The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

Plant development processes are regulated by epigenetic alterations that shape nuclear structure, gene expression, and phenotypic plasticity; these alterations can provide the plant with protection from environmental stresses. During plant growth and development, these processes play a significant role in regulating gene expression to remodel chromatin structure. These epigenetic alterations are mainly regulated by transposable elements (TEs) whose abundance in plant genomes results in their interaction with genomes. Thus, TEs are the main source of epigenetic changes and form a substantial part of the plant genome. Furthermore, TEs can be activated under stress conditions, and activated elements cause mutagenic effects and substantial genetic variability. This introduces novel gene functions and structural variation in the insertion sites and primarily contributes to epigenetic modifications. Altogether, these modifications indirectly or directly provide the ability to withstand environmental stresses. In recent years, many studies have shown that TE methylation plays a major role in the evolution of the plant genome through epigenetic process that regulate gene imprinting, thereby upholding genome stability. The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, leading to genomic stress. These TE-mediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. Thus, TE methylation is essential for plant evolution and stress adaptation, and TEs hold a relevant military position in the plant genome. High-throughput techniques have greatly advanced the understanding of TE-mediated gene expression and its associations with genome methylation and suggest that controlled mobilization of TEs could be used for crop breeding. However, development application in this area has been limited, and an integrated view of TE function and subsequent processes is lacking. In this review, we explore the enormous diversity and likely functions of the TE repertoire in adaptive evolution and discuss some recent examples of how TEs impact gene expression in plant development and stress adaptation.

The Effect of Salt-Tolerant Antagonistic Bacteria CZ-6 on the Rhizosphere Microbial Community of Winter Jujube (Ziziphus jujuba Mill. "Dongzao") in Saline-Alkali Land

As the main economic crop cultivated in the Yellow River Delta, winter jujube contains various nutrients. However, soil salinization and fungal diseases have affected the yield and quality of winter jujube. In order to use plant growth-promoting rhizobacteria (PGPR) to reduce these damages, the antagonistic bacteria CZ-6 isolated from the rhizosphere of wheat in saline soil was selected for experiment. Gene sequencing analysis identified CZ-6 as Bacillus amyloliquefaciens. In order to understand the salt tolerant and disease-resistant effects of CZ-6 strain, determination of related indicators of salt tolerance, pathogen antagonistic tests, and anti-fungal mechanism analyses was carried out. A pot experiment was conducted to evaluate the effect of CZ-6 inoculation on the rhizosphere microbial community of winter jujube. The salt tolerance test showed that CZ-6 strain can survive in a medium with a NaCl concentration of 10% and produces indole acetic acid (IAA) and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase. Studies on the inhibition mechanism of pathogenic fungi show that CZ-6 can secrete cellulase, protease, and xylanase. Gas chromatography-mass spectrometry (GC-MS) analysis showed that CZ-6 can release volatile organic compounds (VOCs), including 2-heptanone and 2-nonanone. In addition, the strain can colonize the rhizosphere and migrate to the roots, stems, and leaves of winter jujube, which is essential for plant growth or defense against pathogens. Illumina MiSeq sequencing data indicated that, compared to the control, the abundance of salt-tolerant bacteria Tausonia in the CZ-6 strain treatment group was significantly increased, while the richness of Chaetomium and Gibberella pathogens was significantly reduced. Our research shows that CZ-6 has the potential as a biological control agent in saline soil. Plant damage and economic losses caused by pathogenic fungi and salt stress are expected to be alleviated by the addition of salt-tolerant antagonistic bacteria.

Continuous Sugarcane Planting Negatively Impacts Soil Microbial Community Structure, Soil Fertility, and Sugarcane Agronomic Parameters

Continuous planting has a negative impact on sugarcane plant growth and reduces global sugarcane crop production, including in China. The response of soil bacteria, fungal, and arbuscular mycorrhizae (AM) fungal communities to continuous sugarcane cultivation has not been thoroughly documented. Using MiSeq sequencing technology, we analyzed soil samples from sugarcane fields with 1, 10, and 30 years of continuous cropping to see how monoculture time affected sugarcane yield, its rhizosphere soil characteristics and microbiota. The results showed that continuous sugarcane planting reduced sugarcane quality and yield. Continuous sugarcane planting for 30 years resulted in soil acidification, as well as C/N, alkali hydrolyzable nitrogen, organic matter, and total sulfur content significantly lower than in newly planted fields. Continuous sugarcane planting affected soil bacterial, fungal, and AM fungal communities, according to PCoA and ANOSIM analysis. Redundancy analysis (RDA) results showed that bacterial, fungal, and AM fungal community composition were strongly associated with soil properties and attributes, e.g., soil AN, OM, and TS were critical environmental factors in transforming the bacterial community. The LEfSe analysis revealed bacterial families (e.g., Gaiellaceae, Pseudomonadaceae, Micromonosporaceae, Nitrosomonadaceae, and Methyloligellaceae) were more prevalent in the newly planted field than in continuously cultivated fields (10 and 30 years), whereas Sphingomonadaceae, Coleofasciculaceae, and Oxyphotobacteria were depleted. Concerning fungal families, the newly planted field was more dominated than the continuously planted field (30 years) with Mrakiaceae and Ceratocystidaceae, whereas Piskurozymaceae, Trimorphomycetaceae, Lachnocladiaceae, and Stigmatodisc were significantly enriched in the continuously planted fields (10 and 30 years). Regarding AMF families, Diversisporaceae was considerably depleted in continuously planted fields (10 and 30 years) compared to the newly planted field. These changes in microbial composition may ultimately lead to a decrease in sugarcane yield and quality in the monoculture system, which provides a theoretical basis for the obstruction mechanism of the continuous sugarcane planting system. However, continuous planting obstacles remain uncertain and further need to be coupled with root exudates, soil metabolomics, proteomics, nematodes, and other exploratory methods.

The Potential Application of Endophytes in Management of Stress from Drought and Salinity in Crop Plants

Endophytic microorganisms present inside the host plant play an essential role in host fitness, nutrient supply and stress tolerance. Endophytes are often used in sustainable agriculture as biofertilizers, biopesticides and as inoculants to mitigate abiotic stresses including salinity, drought, cold and pH variation in the soil. In changing climatic conditions, abiotic stresses create global challenges to achieve optimum crop yields in agricultural production. Plants experience stress conditions that involve endogenous boosting of their immune system or the overexpression of their defensive redox regulatory systems with increased reactive oxygen species (ROS). However, rising stress factors overwhelm the natural redox protection systems of plants, which leads to massive internal oxidative damage and death. Endophytes are an integral internal partner of hosts and have been shown to mitigate abiotic stresses via modulating local or systemic mechanisms and producing antioxidants to counteract ROS in plants. Advancements in omics and other technologies have been made, but potential application of endophytes remains largely unrealized. In this review article, we will discuss the diversity, population and interaction of endophytes with crop plants as well as potential applications in abiotic stress management.

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

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

Biopolymers for Biological Control of Plant Pathogens: Advances in Microencapsulation of Beneficial Microorganisms

The use of biofertilizers, including biocontrol agents such as Pseudomonas and Bacillus in agriculture can increase soil characteristics and plant acquisition of nutrients and enhancement the efficiency of manure and mineral fertilizer. Despite the problems that liquid and solid formulations have in maintaining the viability of microbial agents, encapsulation can improve their application with extended shelf-life, and controlled release from formulations. Research into novel formulation methods especially encapsulation techniques has increased in recent years due to the mounting demand for microbial biological control. The application of polymeric materials in agriculture has developed recently as a replacement for traditional materials and considered an improvement in technological processes in the growing of crops. This study aims to overview of types of biopolymers and methods used for encapsulation of living biological control agents, especially microbial organisms.

Tailoring Next Generation Plant Growth Promoting Microorganisms as Versatile Tools beyond Soil Desalinization: A Road Map towards Field Application

Plant growth promoting bacteria (PGPB) have been the target of intensive research studies toward their efficient use in the field as biofertilizers, biocontrol, and bioremediation agents among numerous other applications. Recent trends in the field of PGPB research led to the development of versatile multifaceted PGPB that can be used in different field conditions such as biocontrol of plant pathogens in metal contaminated soils. Unfortunately, all these research efforts lead to the development of PGPB that failed to perform in salty environments. Therefore, it is urgently needed to address this drawback of these PGPB toward their efficient performance in salinity context. In this paper we provide a review of state-of-the-art research in the field of PGPB and propose a road map for the development of next generation versatile and multifaceted PGPB that can perform in salinity. Beyond soil desalinization, our study paves the way towards the development of PGPB able to provide services in diverse salty environments such as heavy metal contaminated, or pathogen threatened. Smart development of salinity adapted next generation biofertilizers will inevitably allow for mitigation and alleviation of biotic and abiotic threats to plant productivity in salty environments.

Foliar Endophytic Fungi Inhabiting an Annual Grass Along an Aridity Gradient

Mutualistic fungi are known to increase plant tolerance to abiotic and biotic stress. Therefore, it is expected that along aridity gradients the diversity and composition of symbiotic fungal community will be associated with climate. We examined the diversity of foliar endophytic fungi, inhabiting an annual grass, growing in three different climates (arid, Mediterranean, and wet Mediterranean) along the Israeli aridity gradient. Among the identified endophyte taxa, some were unique to each site, some were common to the two sites located in the extremes of the gradient, but none was common to all sites. Although most fungal endophyte taxa identified were not related to stress adaptation, we detected two that are considered to benefit plants by mitigating stress: Cladosporium and Trichoderma. Cladosporium is highly osmotolerant, frequently found in saline environments. Trichoderma is a biocontrol agent, frequently found in mesic environments. These findings support the hypothesis that species composition of foliar endophytic fungi is associated with stress adaptation of plants.

Effect of Bacillus spp. and Brevibacillus sp. on the Photosynthesis and Redox Status of Solanum lycopersicum

Plant-growth-promoting bacteria (PGPB) are gaining attention as a sustainable alternative to current agrochemicals. This study evaluated the impact of three Bacillus spp. (5PB1, 1PB1, FV46) and one Brevibacillus sp. (C9F) on the important crop tomato (Solanum lycopersicum) using the model cv. ‘MicroTom’. The effects of these isolates were assessed on (a) seedlings’ growth and vigor, and (b) adult potted plants. In potted plants, several photosynthetic parameters (chlorophylls (a and b), carotenoids and anthocyanins contents, transpiration rate, stomatal conductance, net CO2 photosynthetic rate, and intercellular CO2 concentration, and on chlorophyll fluorescence yields of light- and dark-adapted leaves)), as well as soluble sugars and starch contents, were quantified. Additionally, the effects on redox status were evaluated. While the growth of seedlings was, overall, not influenced by the strains, some effects were observed on adult plants. The Bacillus safensis FV46 stimulated the content of pigments, compared to C9F. Bacillus zhangzhouensis 5PB1 increased starch levels and was positively correlated with some parameters of the photophosphorylation and the gas exchange phases. Interestingly, Bacillus megaterium 1PB1 decreased superoxide (O2−) content, and B. safensis FV46 promoted non-enzymatic antioxidant defenses, increasing total phenol content levels. These results, conducted on a model cultivar, support the theory that these isolates differently act on tomato plant physiology, and that their activity depends on the age of the plant, and may differently influence photosynthesis. It would now be interesting to analyze the influence of these bacteria using commercial cultivars.

Plant Growth-Promoting Bacteria Improve Growth and Modify Essential Oil in Rose (Rosa hybrida L.) cv. Black Prince

Rose essential oil is rich in compounds widely used by the pharmaceutical and cosmetic industry, due to the biological activities it presents. However, obtaining oil is costly, as the yield per plant is low, which requires several techniques that aim to increase its production. The application of growth-promoting bacteria has been studied for this purpose. Thus, the objective of this work was to select efficient bacteria for production and evaluate their influence on the phytotechnical characteristics and composition of the essential oils of roses. Seven species of bacteria were evaluated for the potential to promote growth in vitro, being tested for nitrogen fixation, phosphate solubilization, protease production and auxin production. From bacteria tested, four were selected and inoculated on rose plants of cultivar Black Prince to evaluate the influence on phytotechnical variables of flower and stem and the oil production. The evaluation of the production of roses was performed through the characteristics of the flowers (size, weight, and diameter of the stem) and floral bud. The essential oils from the inoculated flowers were extracted and evaluated in terms of content, yield, and chemical composition. The application of B. acidiceler, B. subtilis and B. pumilus resulted in flowers with a diameter up to 29% larger. The floral stem was increased by up to 24.5% when B. acidiceler and B. pumilus were used. Meanwhile, the stem diameter was around 41% greater in the presence of B. acidiceler, B. subtilis and in the control. Bacillus pumilus also increased the weight of fresh petals (104%) and essential oil yield (26%), changing the chemical composition of the extracted essential oil. Thus, it is concluded that B. acidiceler, B. pumilus, and B. subtilis improved the phytotechnical characteristics of roses. Among bacteria, B. pumilus increased the essential oil content as well as positively changed the chemical composition of the extracted essential oil.

Small DNA Methylation, Big Player in Plant Abiotic Stress Responses and Memory

DNA methylation is a conserved epigenetic mark that plays important roles in maintaining genome stability and regulating gene expression. As sessile organisms, plants have evolved sophisticated regulatory systems to endure or respond to diverse adverse abiotic environmental challenges, i.e., abiotic stresses, such as extreme temperatures (cold and heat), drought and salinity. Plant stress responses are often accompanied by changes in chromatin modifications at diverse responsive loci, such as 5-methylcytosine (5mC) and N 6-methyladenine (6mA) DNA methylation. Some abiotic stress responses are memorized for several hours or days through mitotic cell divisions and quickly reset to baseline levels after normal conditions are restored, which is referred to as somatic memory. In some cases, stress-induced chromatin marks are meiotically heritable and can impart the memory of stress exposure from parent plants to at least the next stress-free offspring generation through the mechanisms of transgenerational epigenetic inheritance, which may offer the descendants the potential to be adaptive for better fitness. In this review, we briefly summarize recent achievements regarding the establishment, maintenance and reset of DNA methylation, and highlight the diverse roles of DNA methylation in plant responses to abiotic stresses. Further, we discuss the potential role of DNA methylation in abiotic stress-induced somatic memory and transgenerational inheritance. Future research directions are proposed to develop stress-tolerant engineered crops to reduce the negative effects of abiotic stresses.

Comprehensive assessment of growth parameters for screening endophytic bacterial strains in Solanum lycopersicum (Tomato)

Conventional agricultural practices demand application of pesticides for better yield, yet their uncontrolled use for longer duration exhibit deleterious effects on the soil health and subsequent plant productivity. These circumstances have displayed alarming effects on food security in the modern world. Therefore, biological solutions to the crisis can be practiced in consideration to their environmental benefits. Bacterial endophytes are ubiquitous in the phytosystem and beneficial for the plant growth and productivity. The present study aimed to obtain endophytic bacterial strains that can be developed as effective plant growth promoters. For this purpose twelve strains of bacterial endophytes were isolated from different plant sources and their putative plant growth promoting attributes were analyzed by morphological and biochemical studies. Subsequently these isolates were inoculated in the Solanum lycopersicum (Tomato) and the factors like germination percentage, seedling length, biomass production, and leaf variables were analyzed. However, the vigour index was considered as the prime parameter for determining plant growth. In essence, RR2 and RR4 strains were observed as effective growth promoter, hence in future they can be utilized as effective biofertilizers.

A Crosstalk Between Brachypodium Root Exudates, Organic Acids, and Bacillus velezensis B26, a Growth Promoting Bacterium

Plant growth-promoting rhizobacteria (PGPR) are associated with plant roots and use organic compounds that are secreted from root exudates as food and energy source. Root exudates can chemoattract and help bacteria to colonize the surface of plant roots by inducing chemotactic responses of rhizospheric bacteria. In this study, we show that root colonization of Brachypodium distachyon by Bacillus velezensis strain B26 depends on several factors. These include root exudates, organic acids, and their biosynthetic genes, chemotaxis, biofilm formation and the induction of biofilm encoding genes. Analysis of root exudates by GC-MS identified five intermediates of the TCA cycle; malic, fumaric, citric, succinic, oxaloacetic acids, and were subsequently evaluated. The strongest chemotactic responses were induced by malic, succinic, citric, and fumaric acids. In comparison, the biofilm formation was induced by all organic acids with maximal induction by citric acid. Relative to the control, the individual organic acids, succinic and citric acids activated the epsD gene related to EPS biofilm, and also the genes encoding membrane protein (yqXM) and hydrophobin component (bslA) of the biofilm of strain B26. Whereas epsA and epsB genes were highly induced genes by succinic acid. Similarly, concentrated exudates released from inoculated roots after 48 h post-inoculation also induced all biofilm-associated genes. The addition of strain B26 to wild type and to icdh mutant line led to a slight induction but not biologically significant relative to their respective controls. Thus, B26 has no effect on the expression of the ICDH gene, both in the wild type and the mutant backgrounds. Our results indicate that root exudates and individual organic acids play an important role in selective recruitment and colonization of PGPR and inducing biofilm. The current study increases the understanding of molecular mechanisms behind biofilm induction by organic acids.

Organic acids and root exudates of Brachypodium distachyon: effects on chemotaxis and biofilm formation of endophytic bacteria

Root colonization by plant-growth-promoting bacteria could not be useful without the beneficial properties of the bacterium itself. Thus, it is necessary to evaluate the bacterial capacity to form biofilms and establish a successful interaction with the plant roots. We assessed the ability of growth-promoting bacterial strains to form biofilm and display chemotactic behaviour in response to organic acids and (or) root exudates of the model plant Brachypodium distachyon. This assessment was based on the evaluation of single strains of bacteria and a multispecies consortium. The strains coexisted together and formed biofilm under biotic (living root) and abiotic (glass) surfaces. Citric acid stimulated biofilm formation in all individual strains, indicating a strong chemotactic behaviour towards organic acids. Recognizing that the transition from single strains of bacteria to a "multicellular" system would not happen without the presence of adhesion, the alginate and exopolysaccharide (EPS) contents were evaluated. The EPS amounts were comparable in single strains and consortium forms. Alginate production increased 160% in the consortium subjected to drought stress (10% PEG). These findings demonstrated that (i) bacteria-bacteria interaction is the hub of various factors that would not only affect their relation but also could indirectly affect the balanced plant-microbe relation and (ii) root exudates could be very selective in recruiting a highly qualified multispecies consortium.

Study on the correlation between soil microbial diversity and ambient environmental factors influencing the safflower distribution in Xinjiang

The effects of soil microbial properties and physiographical factors on safflower distributions in the main safflower plantations of Xinjiang province in China were studied. This study may help determine the basis of the environmental factors for evaluating the geoherbalism of this medicinal plant. The soil microbial biodiversity in the bulk soil and rhizosphere of safflower at different growth stages and from different sampling plots were characterized by analyzing the environmental DNAs in the samples. With general primers targeting the 16S ribosomal DNA for bacteria and the internal transcribed spacer 1 gene for fungi, the study was performed using marker gene amplification coupled with Illumina HiSeq high-throughput sequencing technologies. Correlation analysis and a distance-based redundancy analysis were performed to determine the dominant factors affecting the distribution of the microorganism in safflower soils. A total of 16517 bacterial operational taxonomic units (OTUs) were obtained from all the 108 soil samples of nine safflower sampling plots. At the phylum level, 48 phyla have been identified with Actinobacteria (32.9%) and proteobacteria (28.7%) being predominant. For fungi, 8746 OTUs were obtained, which belonged to seven phyla with Ascomycota overwhelmingly superior in relative abundance. A significant positive correlation was found between soil microbe quantity and ASL (above sea level). Safflower was sensitive to changes in elevation, growing more abundantly in the mountainous regions at heights of around 1,200 m above sea level. It is concluded that the dominant factors affecting the distribution of microorganisms in safflower soils were soil moisture, available N, and ASL.

Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications

The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.

Bacillus subtilis strain GOT9 confers enhanced tolerance to drought and salt stresses in Arabidopsis thaliana and Brassica campestris

Soil is a primary source of water and inorganic nutrients vital for plant growth. In particular, the rhizosphere, a microecological region around the plant roots, is enriched with root exudates that enable beneficial microbial communities to form. Plant growth-promoting rhizobacteria (PGPR) are rhizosphere bacteria that contribute to the improvement of plant growth through diverse physiological mechanisms. Identifying PGPR is beneficial for agriculture because their use can effectively increase the productivity of plants without the harmful side effects of chemical fertilizers. To further enrich the pool of PGPR that contribute to abiotic stress resistance in plants, we screened roughly 491 bacteria that had previously been isolated in soil from Gotjawal in Jeju island, South Korea. Among several candidates, the application of Bacillus subtilis strain GOT9, led to the enhancement of drought and salt stress tolerance in Arabidopsis. In agreement with the increased stress tolerance phenotypes, its application resulted in increases in the transcripts of various drought stress- and salt stress-inducible genes in the absence or presence of the stresses. Furthermore, the treatment resulted in improved lateral root growth and development in Arabidopsis. GOT9 also led to enhanced tolerance against drought and salt stresses and to upregulation of drought-inducible genes in Brassica, a closely related crop to Arabidopsis. Taken together, these results show that GOT9 could be utilized as a biotic resource that effectively minimizes damage to plants from environmental stresses.

Isolation and Characterization of Biosurfactant-Producing Bacteria From Oil Well Batteries With Antimicrobial Activities Against Food-Borne and Plant Pathogens

Microbial biosurfactants, produced by fungi, yeast, and bacteria, are surface-active compounds with emulsifying properties that have a number of known activities, including the solubilization of microbial biofilms. In an on-going survey to uncover new or enhanced antimicrobial metabolite-producing microbes from harsh environments, such as oil-rich niches, 123 bacterial strains were isolated from three oil batteries in the region of Chauvin, Alberta, and characterized by 16S rRNA gene sequencing. Based on their nucleotide sequences, the strains are associated with 3 phyla (Actinobacteria, Proteobacteria and Firmicutes), as well as 17 other discrete genera that shared high homology with known sequences, with the majority of these strains identified to the species level. The most prevalent strains associated with the three oil wells belonged to the Bacillus genus. Thirty-four of the 123 strains were identified as biosurfactant-producers, among which Bacillus methylotrophicus strain OB9 exhibited the highest biosurfactant activity based on multiple screening methods and a comparative analysis with the commercially available biosurfactant, Tween 20. B. methylotrophicus OB9 was selected for further antimicrobial analysis and addition of live cultures of B. methylotrophicus OB9 (or partially purified biosurfactant fractions thereof) were highly effective on biofilm disruption in agar diffusion assays against several Gram-negative food-borne bacteria and plant pathogens. Upon co-culturing with B. methylotrophicus OB9, the number of either Salmonella enterica subsp. enterica Newport SL1 or Xanthomonas campestris B07.007 cells significantly decreased after 6 h and were not retrieved from co-cultures following 12 h exposure. These results also translated to studies on plants, where bacterized tomato seedlings with OB9 significantly protected the tomato leaves from Salmonella enterica Newport SL1 contamination, as evidenced by a 40% reduction of log10 CFU of Salmonella/mg leaf tissue compared to non-bacterized tomato leaves. When B. methylotrophicus 0B9 was used for bacterized lettuce, the growth of X. campestris B07.007, the causal agent of bacterial leaf spot of lettuce, was completely inhibited. While limited, these studies are noteworthy as they demonstrate the inhibition spectrum of B. methylotrophicus 0B9 against both human and plant pathogens; thereby making this bacterium attractive for agricultural and food safety applications in a climate where microbial-biofilm persistence is an increasing problem.

Endophytic Bacterial Microbiome Diversity in Early Developmental Stage Plant Tissues of Wheat Varieties

Endophytic bacteria are an important part of different functions in plants that lead to plants’ production characteristics as well as their stress response mechanisms. Endophytic bacterial diversity was analyzed in this study to describe 16S rRNA variability and changes in the leaves of drought-tolerant and drought-susceptible wheat when growth under in vitro conditions. A metagenomic analysis was applied and a pilot exploratory study was performed to prove this type of analysis as applicable to tracking endophytic bacterial diversity changes when a drought stress is applied to an in vitro culture of wheat. The study showed that the changes in the bacterial endophytes’ variabilities associated preferentially with the drought stress varietal characteristics of the analyzed wheat instead of the applied stress conditions.

Plant Growth Promoting Rhizobacterial Mitigation of Drought Stress in Crop Plants: Implications for Sustainable Agriculture

Abiotic stresses arising from climate change negates crop growth and yield, leading to food insecurity. Drought causes oxidative stress on plants, arising from excessive production of reactive oxygen species (ROS) due to inadequate CO2, which disrupts the photosynthetic machinery of plants. The use of conventional methods for the development of drought-tolerant crops is time-consuming, and the full adoption of modern biotechnology for crop enhancement is still regarded with prudence. Plant growth-promoting rhizobacteria (PGPR) could be used as an inexpensive and environmentally friendly approach for enhancing crop growth under environmental stress. The various direct and indirect mechanisms used for plant growth enhancement by PGPR were discussed. Synthesis of 1-aminocyclopropane−1-carboxylate (ACC) deaminase enhances plant nutrient uptake by breaking down plant ACC, thereby preventing ethylene accumulation, and enable plants to tolerate water stress. The exopolysaccharides produced also improves the ability of the soil to withhold water. PGPR enhances osmolyte production, which is effective in reducing the detrimental effects of ROS. Multifaceted PGPRs are potential candidates for biofertilizer production to lessen the detrimental effects of drought stress on crops cultivated in arid regions. This review proffered ways of augmenting their efficacy as bio-inoculants under field conditions and highlighted future prospects for sustainable agricultural productivity.

Genetic Screening and Expression Analysis of Psychrophilic Bacillus spp. Reveal Their Potential to Alleviate Cold Stress and Modulate Phytohormones in Wheat

Abiotic stress in plants pose a major threat to cereal crop production worldwide and cold stress is also notorious for causing a decrease in plant growth and yield in wheat. The present study was designed to alleviate cold stress on plants by inoculating psychrophilic PGPR bacteria belonging to Bacillus genera isolated from extreme rhizospheric environments of Qinghai-Tibetan plateau. The genetic screening of psychrophilic Bacillus spp. CJCL2, RJGP41 and temperate B. velezensis FZB42 revealed presence of genetic features corresponding to cold stress response, membrane transport, signal transduction and osmotic regulation. Subsequently, the time frame study for the expression of genes involved in these pathways was also significantly higher in psychrophilic strains as analyzed through qPCR analysis at 4 ℃. The inoculated cold tolerant Bacillus strains also aided in inducing stress response in wheat by regulating abscisic acid, lipid peroxidation and proline accumulation pathways in a beneficial manner. Moreover, during comparative analysis of growth promotion in wheat all three Bacillus strains showed significant results at 25 ℃. Whereas, psychrophilic Bacillus strains CJCL2 and RJGP41 were able to positively regulate the expression of phytohormones leading to significant improvement in plant growth under cold stress.

Transcriptional alterations reveal Bacillus amyloliquefaciens-rice cooperation under salt stress

The Bacillus amyloliquefaciens-SN13 and model crop rice (Oryza sativa) were chosen to understand the complex regulatory networks that govern plant-PGPR interaction under salt stress. During stress, inoculation with SN13 significantly increased biomass, relative water content, proline and total soluble sugar in rice while decreased lipid peroxidation and electrolyte leakage. Extensive alterations in gene expression were also observed in rice root transcriptome under stress in the presence of SN13. Rhizobacteria induced changes in expression of a considerable number of photosynthesis, hormone, and stress-responsive genes, in addition to cell-wall and lipid metabolism-related genes under salt stress as compared to salt stress or SN13 inoculation alone, indicating its potential role in reducing the harmful effects of salinity. To validate RNA-seq data, qRT-PCR was performed for selected differentially expressed genes representing various functional categories including metabolism, regulation, stress-response, and transporters. Results indicate qualitative and quantitative differences between roots responses to SN13 under stressed and unstressed conditions. Functional expressions of OsNAM and OsGRAM in yeast showed enhanced tolerance to various abiotic stresses, indicating crucial SN13-rice interaction in imparting beneficial effects under stress. This is first detailed report on understanding molecular mechanism underlying beneficial plant-microbe interaction in any economically important model crop plant under abiotic stress.