In-depth genome analysis of Bacillus sp. BH32, a salt stress-tolerant endophyte obtained from a halophyte in a semiarid region

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.

Effect of environmental stress factors on the expression of virulence genes and pathogenicity of lethal Bacillus cereus of bovine origin

Objective

Bacillus cereus (B. cereus) can be used as a probiotic or produce a variety of toxins that are pathogenic to humans and animals. Environmental stressors can affect the growth process of B. cereus and the expression of its virulence genes. Due to the limitations of methods such as pharmacological disinfection methods (there are limits to the use of antibiotics) and chemical disinfection methods (chemical methods may produce residues), attempts can be made to remove and reduce B. cereus infections through environmental stress factors.

Methods

In this study, the expression of four virulence genes (nheA, hblD, cytK, and entFM) of bovine-origin lethal B. cereus was investigated by qPCR under the effect of different environmental stressors. The extent of pathological damage to various organs of mice by B. cereus was observed by pathological sections.

Results

The results showed that high temperature could inhibit the expression of B. cereus virulence genes. Expression of B. cereus virulence genes was affected under the influence of pH. Different salt concentrations could make the B. cereus virulence genes show low expression. Under a single environmental stressors, nheA, hblD, cytK, and entFM had the lowest expression at 40°C, pH 8.0, and were lowly expressed at all salt concentrations except the control group. The action of multiple environmental stressors affect the expression of virulence genes. Under multiple environmental stressors, nheA, hblD and cytK were least expressed at a temperature of 40°C, pH 6.0, and salt concentration of 3.0%, and entFM was least expressed at a temperature of 20°C, pH 8.0, and salt concentration of 1.5%. Animal pathogenicity tests have shown that environmental stressors affect the virulence of B. cereus.

Conclusion

The level of virulence gene expression in B. cereus can be reduced by environmental stress factors, thus further reducing the risk of B. cereus to human health. This study provides some reference for the prevention and control of B. cereus disease.

Drought and salt stress mitigation in crop plants using stress-tolerant auxin-producing endophytic bacteria: a futuristic approach towards sustainable agriculture

Abiotic stresses, especially drought stress and salt stress in crop plants are accelerating due to climate change. The combined impact of drought and salt is anticipated to lead to the loss of up to 50% of arable land globally, resulting in diminished growth and substantial yield losses threatening food security. Addressing the challenges, agriculture through sustainable practices emerges as a potential solution to achieve Zero Hunger, one of the sustainable development goals set by the IUCN. Plants deploy a myriad of mechanisms to effectively address drought and salt stress with phytohormones playing pivotal roles as crucial signaling molecules for stress tolerance. The phytohormone auxin, particularly indole acetic acid (IAA) emerges as a paramount regulator integral to numerous aspects of plant growth and development. During both drought and salt stress conditions, auxin plays crucial roles for tolerance, but stress-induced processes lead to decreased levels of endogenous free auxin in the plant, leading to an urgent need for auxin production. With an aim to augment this auxin deficiency, several researchers have extensively investigated auxin production, particularly IAA by plant-associated microorganisms, including endophytic bacteria. These endophytic bacteria have been introduced into various crop plants subjected to drought or salt stress and potential isolates promoting plant growth have been identified. However, post-identification, essential studies on translational research to advance these potential isolates from the laboratory to the field are lacking. This review aims to offer an overview of stress tolerant auxin-producing endophytic bacterial isolates while identifying research gaps that need to be fulfilled to utilize this knowledge for the formulation of crop-specific and stress-specific endophyte bioinoculants for the plant to cope with auxin imbalance occurring during these stress conditions.

Genomic and phenotypic characterisation of Enterococcus mundtii AM_AQ_BC8 for its anti-biofilm, antimicrobial and probiotic potential

Enterococcus mundtii AM_AQ_BC8 isolated from biofouled filtration membrane was characterised as a potential probiotic bacterium showing strong L-lactic acid-producing capability. Experimental studies revealed that E. mundtii AM_AQ_BC8 possess antibiofilm and antimicrobial ability too, as tested against strong biofilm-forming bacteria like Pseudomonas spp. The present study has evaluated the genetic potential of E. mundtii AM_AQ_BC8 through genome sequencing. Whole genome analysis revealed the presence of key genes like ldh_1 and ldh_2 responsible for lactic acid production along with genes encoding probiotic features such as acid and bile salt resistance (dnaK, dnaJ, argS), fatty acid synthesis (fabD, fabE) and lactose utilisation (lacG, lacD). The phylogenomic analysis based on OrthoANI (99.85%) and dDDH (96.8%) values revealed that the strain AM_AQ_BC8 shared the highest homology with E. mundtii. The genome sequence of strain AM_AQ_BC8 has been deposited to NCBI and released with GenBank accession no. SAMN32531201. The study primarily demonstrated the probiotic potential of E. mundtii AM_AQ_BC8 isolate, for L-lactate synthesis in high concentration (8.98 g/L/day), which also showed anti-biofilm and antimicrobial activities.

Organization, conservation, and diversity of biosynthetic gene clusters in Bacillus sp. BH32 and its closest relatives in the Bacillus cereus group

This study explores the organization, conservation, and diversity of biosynthetic gene clusters (BGCs) among Bacillus sp. strain BH32, a plant-beneficial bacterial endophyte, and its closest nontype Bacillus cereus group strains. BGC profiles were predicted for each of the 17 selected strains using antiSMASH, resulting in the detection of a total of 198 BGCs. We quantitatively compared the BGCs and analysed their conservation, distribution, and evolutionary relationships. The study identified both conserved and singleton BGCs across the studied Bacillus strains, with minimal variation, and discovered two major BGC synteny blocks composed of homologous BGCs conserved within the B. cereus group. The identified BGC synteny blocks provide insight into the evolutionary relationships and diversity of BGCs within this complex group.

In Silico Safety Assessment of Bacillus Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates

Bacillus species isolated from Polish bee pollen (BP) and bee bread (BB) were characterized for in silico probiotic and safety attributes. A probiogenomics approach was used, and in-depth genomic analysis was performed using a wide array of bioinformatics tools to investigate the presence of virulence and antibiotic resistance properties, mobile genetic elements, and secondary metabolites. Functional annotation and Carbohydrate-Active enZYmes (CAZYme) profiling revealed the presence of genes and a repertoire of probiotics properties promoting enzymes. The isolates BB10.1, BP20.15 (isolated from bee bread), and PY2.3 (isolated from bee pollen) genome mining revealed the presence of several genes encoding acid, heat, cold, and other stress tolerance mechanisms, adhesion proteins required to survive and colonize harsh gastrointestinal environments, enzymes involved in the metabolism of dietary molecules, antioxidant activity, and genes associated with the synthesis of vitamins. In addition, genes responsible for the production of biogenic amines (BAs) and D-/L-lactate, hemolytic activity, and other toxic compounds were also analyzed. Pan-genome analyses were performed with 180 Bacillus subtilis and 204 Bacillus velezensis genomes to mine for any novel genes present in the genomes of our isolates. Moreover, all three isolates also consisted of gene clusters encoding secondary metabolites.

Mechanism of Salt Tolerance and Plant Growth Promotion in Priestia megaterium ZS-3 Revealed by Cellular Metabolism and Whole-Genome Studies

Approximately one-third of agricultural land worldwide is affected by salinity, which limits the productivity and sustainability of crop ecosystems. Plant-growth-promoting rhizobacteria (PGPR) are a potential solution to this problem, as PGPR increases crop yield through improving soil fertility and stress resistance. Previous studies have shown that Priestia megaterium ZS-3(ZS-3) can effectively help plants tolerate salinity stress. However, how ZS-3 regulates its metabolic adaptations in saline environments remains unclear. In this study, we monitored the metabolic rearrangement of compatibilisers in ZS-3 and combined the findings with genomic data to reveal how ZS-3 survives in stressful environments, induces plant growth, and tolerates stress. The results showed that ZS-3 tolerated salinity levels up to 9%. In addition, glutamate and trehalose help ZS-3 adapt to osmotic stress under low NaCl stress, whereas proline, K+, and extracellular polysaccharides regulate the osmotic responses of ZS-3 exposed to high salt stress. Potting experiments showed that applying the ZS-3 strain in saline and neutral soils could effectively increase the activities of soil acid phosphatase, urease, and invertase in both soils, thus improving soil fertility and promoting plant growth. In addition, strain ZS-3-GFP colonised the rhizosphere and leaves of Cinnamomum camphora well, as confirmed by confocal microscopy and resistance plate count analysis. Genomic studies and in vitro experiments have shown that ZS-3 exhibits a variety of beneficial traits, including plant-promoting, antagonistic, and other related traits (such as resistance to saline and heavy metal stress/tolerance, amino acid synthesis and transport, volatile compound synthesis, micronutrient utilisation, and phytohormone biosynthesis/regulatory potential). The results support that ZS-3 can induce plant tolerance to abiotic stresses. These data provide important clues to further reveal the interactions between plants and microbiomes, as well as the mechanisms by which micro-organisms control plant health.

Genome insights into the plant growth-promoting bacterium Saccharibacillus brassicae ATSA2T

Endophytes can facilitate the improvement of plant growth and health in agriculturally important crops, yet their genomes and secondary metabolites remain largely unexplored. We previously isolated Saccharibacillus brassicae strain ATSA2^T from surface-sterilized seeds of kimchi cabbage and represented a novel species of the genus Saccharibacillus. In this study, we evaluated the plant growth-promoting (PGP) effect of strain ATSA2^T in kimchi cabbage, bok choy, and pepper plants grown in soils. We found a significant effect on the shoot and root biomass, and chlorophyll contents following strain ATSA2^T treatment. Strain ATSA2^T displayed PGP traits such as indole acetic acid (IAA, 62.9 μg/mL) and siderophore production, and phosphate solubilization activity. Furthermore, genome analysis of this strain suggested the presence of gene clusters involved in iron acquisition (fhuABD, afuABC, fbpABC, and fepCDG) and phosphate solubilization (pstABCHS, phoABHLU, and phnCDEP) and other phytohormone biosynthesis genes, including indole-3-acetic acid (trpABCDEFG), in the genome. Interestingly, the secondary metabolites cerecidin, carotenoid, siderophore (staphylobactin), and bacillaene underlying plant growth promotion were found in the whole genome via antiSMASH analysis. Overall, physiological testing and genome analysis data provide comprehensive insights into plant growth-promoting mechanisms, suggesting the relevance of strain ATSA2^T in agricultural biotechnology.

Salinity stress endurance of the plants with the aid of bacterial genes

The application of plant growth-promoting bacteria (PGPB) is vital for sustainable agriculture with continuous world population growth and an increase in soil salinity. Salinity is one of the severe abiotic stresses which lessens the productivity of agricultural lands. Plant growth-promoting bacteria are key players in solving this problem and can mitigate salinity stress. The highest of reported halotolerant Plant growth-promoting bacteria belonged to Firmicutes (approximately 50%), Proteobacteria (40%), and Actinobacteria (10%), respectively. The most dominant genera of halotolerant plant growth-promoting bacteria are Bacillus and Pseudomonas. Currently, the identification of new plant growth-promoting bacteria with special beneficial properties is increasingly needed. Moreover, for the effective use of plant growth-promoting bacteria in agriculture, the unknown molecular aspects of their function and interaction with plants must be defined. Omics and meta-omics studies can unreveal these unknown genes and pathways. However, more accurate omics studies need a detailed understanding of so far known molecular mechanisms of plant stress protection by plant growth-promoting bacteria. In this review, the molecular basis of salinity stress mitigation by plant growth-promoting bacteria is presented, the identified genes in the genomes of 20 halotolerant plant growth-promoting bacteria are assessed, and the prevalence of their involved genes is highlighted. The genes related to the synthesis of indole acetic acid (IAA) (70%), siderophores (60%), osmoprotectants (80%), chaperons (40%), 1-aminocyclopropane-1-carboxylate (ACC) deaminase (50%), and antioxidants (50%), phosphate solubilization (60%), and ion homeostasis (80%) were the most common detected genes in the genomes of evaluated halotolerant plant growth-promoting and salinity stress-alleviating bacteria. The most prevalent genes can be applied as candidates for designing molecular markers for screening of new halotolerant plant growth-promoting bacteria.

Transcriptome analysis reveals the molecular mechanism of cinnamaldehyde against Bacillus cereus spores in ready-to-eat beef

The purpose of this study was to investigate the antibacterial effect and mechanism of cinnamaldehyde on Bacillus cereus spores in ready-to-eat beef. The colour difference and texture of the ready-to-eat beef supplemented with cinnamaldehyde did not differ greatly from the colour and texture of the blank beef. However, cinnamaldehyde has an effective antibacterial effect on the total number of bacterial colonies and B. cereus spores in ready-to-eat beef. Transmission electron microscopy (TEM) analysis revealed that the cell membrane of B. cereus was disrupted by cinnamaldehyde, leading to leakage of intracellular components. Transcriptome sequencing (RNA-seq) indicated that the B. cereus spore resistance regulation system (sigB, sigW, rsbW, rsbV, yfkM and yflT) and phosphoenolpyruvate phosphotransferase system (PTS) (ptsH, ptsI and ptsG) respond positively to cinnamaldehyde in an adverse environment. Intracellular disorders due to damage to the cell membrane involve some transporters (copA, opuBA and opuD) and some oxidative stress systems (ywrO, scdA and katE) in the regulation of the body. However, downregulation of K⁺ transport channels (kdpD and kdpB), osmotic pressure regulation (opuE) and some oxidative stress (norR and srrA)-related genes may accelerate spore apoptosis. In addition, cinnamaldehyde also effectively inhibits the spore germination-related genes (smc, mreB and gerE). This study provides new insights into the molecular mechanism of the antibacterial effect of cinnamaldehyde on B. cereus spores in ready-to-eat beef.