Biocontrol traits of Bacillus licheniformis GL174, a culturable endophyte of Vitis vinifera cv. Glera

Microbiome alterations in primary Sjögren's syndrome: Regional dysbiosis and microbiome-targeted therapeutic strategies

Primary Sjögren's syndrome (pSS) is a complex autoimmune disease characterized by diverse clinical manifestations. While xerophthalmia and xerostomia are hallmark symptoms, the disease often involves multiple organ systems, including the kidneys, lungs, nervous system, and gastrointestinal tract, leading to systemic morbidity in severe cases. Despite extensive research, the precise pathogenesis of pSS remains unclear, likely involving infectious, hormonal, and genetic factors. Emerging evidence highlights the microbiome as a key contributor to autoimmune diseases, including pSS. Dysbiosis in the oral, ocular, gut, and genital microbiomes plays a critical role in disease onset, progression, and variability. This review summarizes current findings on microbiome alterations in pSS, emphasizing their role in pathogenesis and clinical features, and explores microbiome-targeted therapies. Understanding the role of the microbiome in pSS pathophysiology could advance disease management and inspire targeted therapeutic strategies.

Isolation and Functional Characterization of Endophytic Bacteria from Muscadine Grape Berries: A Microbial Treasure Trove

Muscadine grapes are renowned for their unique traits, natural disease resistance, and rich bioactive compounds. Despite extensive research on their phytochemical properties, microbial communities, particularly endophytic bacteria, remain largely unexplored. These bacteria play crucial roles in plant health, stress tolerance, and ecological interactions. This study represents the first comprehensive effort to isolate, identify, and functionally characterize the bacterial endophytes inhabiting muscadine grape berries using a culture-dependent approach. We isolated diverse bacterial species spanning six genera-Bacillus, Staphylococcus, Paenibacillus, Calidifontibacillus, Curtobacterium, and Tatumella. Microscopic and physiological analysis revealed variations in bacterial morphology, with isolates demonstrating adaptability to varied temperatures. Cluster-based analysis indicated functional specialization among the isolates, with species from Pseudomonadota and Actinomycetota exhibiting superior plant growth-promoting abilities, whereas Bacillota species displayed potential biocontrol and probiotic properties. Among them, Tatumella ptyseos demonstrated exceptional plant growth-promoting traits, including indole-3-acetic acid production, nitrogen fixation, phosphate solubilization, and carbohydrate fermentation. Additionally, Bacillus spp. showed presumptive biocontrol potential, while Paenibacillus cineris emerged as a potential probiotic candidate. The identification of Calidifontibacillus erzurumensis as a novel endophytic species further expands the known biodiversity of grape-associated microbes. These findings provide insights into the metabolic diversity and functional roles of muscadine grape-associated endophytes, highlighting their potential for agricultural and biotechnological applications.

Antifungal efficacy and mechanisms of Bacillus licheniformis BL06 against Ceratocystis fimbriata

Sweet potato black rot caused by the pathogenic fungus Ceratocystis fimbriata is a destructive disease that can result in severe agricultural losses. This study explores the antifungal efficacy and underlying mechanisms of Bacillus licheniformis BL06 against C. fimbriata. The plate antagonism assay revealed that BL06 significantly suppressed the radial growth of C. fimbriata mycelia, achieving inhibition rates of 39.53%, 53.57%, 64.38%, and 69.11% after 7, 10, 13, and 16 days, respectively. In vivo experiments demonstrated that BL06-treated sweet potato tissues exhibited markedly smaller lesions than the control, indicating effective suppression of black rot. Microscopic observations indicated that BL06 treatment altered the morphology and activity of C. fimbriata mycelia, causing swelling and deformation. Additionally, BL06 markedly reduced spore production and germination in a dose-dependent manner, with complete inhibition observed at the highest concentrations tested. The cell-free supernatant (CFS) of BL06 was identified as the primary antifungal agent, achieving an inhibition rate of 76.11% on mycelial growth. Transcriptome analysis of C. fimbriata treated with BL06 CFS revealed significant downregulation of genes involved in cell wall and membrane biosynthesis, spore development, protein processing in the endoplasmic reticulum, and energy metabolism. These findings suggest that BL06 is a potent biocontrol agent against C. fimbriata, exerting its effects through multiple molecular pathways.

Biocontrol efficacy of Bacillus licheniformis and Bacillus amyloliquefaciens against rice pathogens

Biocontrol is a cost-effective and eco-friendly approach to control plant pathogens using natural enemies. Antagonistic microorganisms or their derivatives specifically target the plant pathogens while minimizing the harm to non-target organisms. Bacterial blight and brown spot are the major rice diseases caused by Xanthomonas oryzae pv. oryzae (Xoo) and Bipolaris oryzae (Bo), respectively. This study was conducted to assess the plant growth-promoting potential and biocontrol activity of root-associated bacteria against the rice pathogens, Xoo and Bo. A total of 98 bacteria were isolated from rice roots and characterized for plant growth-promoting properties including phosphate solubilization, indole-3-acetic acid production, nitrogen fixation and biofilm formation. Based on these properties, 36 bacteria were selected and tested for biocontrol potential against rice pathogens via co-culturing antagonism assay. LE7 exhibited the maximum inhibition of 79%, while FR8, PE2, LE7, LR22 and LR28 also significantly reduced the growth of Xoo. Likewise, FR2, LR22, LR35 and LE7 significantly inhibited the growth of Bo, in which LR22 exhibited the maximum inhibition of 81%. Under controlled-conditions, LE7 and LR22 significantly reduced the disease incidence of Xoo and Bo, respectively, and improved the growth of rice. Full-length 16S rRNA gene sequencing of most potential bacterial isolates, LE7 and LR22, revealed their maximum identity with Bacillus amyloliquefaciens and Bacillus licheniformis, respectively. Application of Bacillus spp. as biocontrol agent represents enormous potential in rice farming. The most promising bacterial isolates could be used as bioinoculants for rice disease management and improved production in a sustainable manner.

Insights on mining the pangenome of Sphingobacterium thalpophilum NMS02 S296 from the resistant banana cultivar Pisang lilin confirms the antifungal action against Fusarium oxysporum f. sp. cubense

Introduction

Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense (Foc), poses a significant global threat to banana cultivation. Conventional methods of disease management are increasingly challenged, thus making it necessary to explore alternative strategies. Bacterial endophytes, particularly from resistant genotypes, are gaining attention as potential biocontrol agents. Sphingobacterium thalpophilum, isolated from the resistant banana cultivar Pisang lilin (JALHSB010000001-JALHSB010000029), presents an intriguing prospect for combating Fusarium wilt. However, its underlying biocontrol mechanisms remain poorly understood. This study aimed to elucidate the antifungal efficacy of S. thalpophilum NMS02 S296 against Foc and explore its biocontrol mechanisms at the genomic level.

Methods

Whole genome sequencing of S. thalpophilum NMS02 S296 was conducted using next-generation sequencing technologies and bioinformatics analyses were performed to identify genes associated with antifungal properties. In vitro assays were used to assess the inhibitory effects of the bacterial isolate on the mycelial growth of Foc. To explore the biomolecules responsible for the observed antagonistic activity, metabolites diffused into the agar at the zone of inhibition between Foc S16 and S. thalpophilum NMS02 S296 were extracted and identified.

Results

Whole genome sequencing revealed an array of genes encoding antifungal enzymes and secondary metabolites in S. thalpophilum NMS02 S296. In vitro experiments demonstrated significant inhibition of Foc mycelial growth by the bacterial endophyte. Comparative genomic analysis highlighted unique genomic features in S. thalpophilum linked to its biocontrol potential, setting it apart from other bacterial species.

Discussion

The study underscores the remarkable antifungal efficacy of S. thalpophilum NMS02 S296 against Fusarium wilt. The genetic basis for its biocontrol potential was elucidated through whole genome sequencing, shedding light on the mechanisms behind its antifungal activity. This study advanced our understanding of bacterial endophytes as biocontrol agents and offers a promising avenue for plant growth promotion towards sustainable strategies to mitigate Fusarium wilt in banana cultivation.

Bacillus licheniformisYB06: A Rhizosphere-Genome-Wide Analysis and Plant Growth-Promoting Analysis of a Plant Growth-Promoting Rhizobacterium Isolated from Codonopsis pilosula

Codonopsis pilosula, commonly known as Dangshen, is a valuable medicinal plant, but its slow growth and susceptibility to environmental stress pose challenges for its cultivation. In pursuit of sustainable agricultural practices to enhance the yield and quality of Dangshen, the present study isolated a bacterial strain exhibiting plant growth-promoting potential from the rhizosphere of C. pilosula. This strain was subsequently identified as Bacillus licheniformisYB06. Assessment of its plant growth-promoting attributes revealed the potential of B. licheniformis YB06 as a biofertilizer. Whole-genome sequencing of B. licheniformis YB06 revealed a genome size of 4,226,888 bp with a GC content of 46.22%, harboring 4325 predicted protein-coding sequences. Genomic analysis of B. licheniformis YB06 revealed a diverse array of genes linked to induced systemic resistance (ISR) and plant growth-promoting (PGP) traits, encompassing phytohormone production, nitrogen assimilation and reduction, siderophore biosynthesis, phosphate solubilization, biofilm formation, synthesis of PGP-related amino acids, and flagellar motility. Seed germination assays demonstrated the positive effects of B. licheniformis YB06 on the germination and growth of C. pilosula seedlings. Furthermore, we explored various fertilization regimes, particularly the B. licheniformis YB06-based biofertilizer, were investigated for their impact on the structure and diversity of the C. pilosula rhizosphere soil bacterial community. Our findings revealed that fertilization significantly impacted soil bacterial composition and diversity, with the combined application of B. licheniformis YB06-based biofertilizer and organic fertilizer exhibiting a particularly pronounced enhancement of rhizosphere bacterial community structure and diversity. This study represents the first report on the beneficial effects of B. licheniformis YB06 on both the growth of C. pilosula and the composition of its rhizosphere soil microbial community. These findings provide a theoretical foundation and practical guidance for the development of novel bio-organic compound fertilizers, thereby contributing to the sustainable cultivation of C. pilosula.

The potential of enhanced phytoremediation to clean up multi-contaminated soil - insights from metatranscriptomics

This study aimed to (i) investigate the potential for enhanced phytoremediation to remove contaminants from soil historically co-contaminated with petroleum hydrocarbons (PHs) and heavy metals (HMs) and (ii) analyze the expression of crucial bacterial genes and whole metatranscriptomics profiles for better understanding of soil processes during applied treatment. Phytoremediation was performed using Zea mays and supported by the Pseudomonas qingdaonensis ZCR6 strain and a natural biofertilizer: meat and bone meal (MBM). In previous investigations, mechanisms supporting plant growth and PH degradation were described in the ZCR6 strain. Here, ZCR6 survived in the soil throughout the experiment, but the efficacy of PH removal from all soils fertilized with MBM reached 32 % regardless of the bacterial inoculation. All experimental groups contained 2 % (w/w) MBM. The toxic effect of this amendment on plants was detected 30 days after germination, irrespective of ZCR6 inoculation. Among the 17 genes tested using the qPCR method, only expression of the acdS gene, encoding 1-aminocyclopropane-1-carboxylic acid deaminase, and the CYP153 gene, encoding cytochrome P450-type alkane hydroxylase, was detected in soils. Metatranscriptomic analysis of soils indicated increased expression of methane particulated ammonia monooxygenase subunit A (pmoA-amoA) by Nitrosomonadales bacteria in all soils enriched with MBM compared to the non-fertilized control. We suggest that the addition of 2 % (w/w) MBM caused the toxic effect on plants via the rapid release of ammonia, and this led to high pmoA-amoA expression. In parallel, due to its wide substrate specificity, enhanced bacterial hydrocarbon removal in MBM-treated soils was observed. The metatranscriptomic results indicate that MBM application should be considered to improve bioremediation of soils polluted with PHs rather than phytoremediation. However, lower concentrations of MBM could be considered for phytoremediation enhancement. From a broader perspective, these results indicated the superior capability of metatranscriptomics to investigate the microbial mechanisms driving various bioremediation techniques.

Insights into soil nematode diversity and bacterial community of Thai jasmine rice rhizosphere from different paddy fields in Thailand

Globally, phytonematodes cause significant crop losses. Understanding the functions played by the plant rhizosphere soil microbiome during phytonematodes infection is crucial. This study examined the distribution of phytonematodes in the paddy fields of five provinces in Thailand, as well as determining the keystone microbial taxa in response to environmental factors that could be considered in the development of efficient biocontrol tactics in agriculture. The results demonstrated that Meloidogyne graminicola and Hirschmanniella spp. were the major and dominant phytonematodes distributed across the paddy fields of Thailand. Soil parameters (total P, Cu, Mg, and Zn) were the important factors affecting the abundance of both nematodes. Illumina next-generation sequencing demonstrated that the levels of bacterial diversity among all locations were not significantly different. The Acidobacteriota, Proteobacteria, Firmicutes, Actinobacteriota, Myxococcota, Chloroflexi, Verrucomicrobiota, Bacteroidota, Gemmatimonadota, and Desulfobacterota were the most abundant bacterial phyla observed at all sites. The number of classes of the Acidobacteriae, Clostridia, Bacilli, and Bacteroidia influenced the proportions of Hirschmanniella spp., Tylenchorhynchus spp., and free-living nematodes in the sampling dirt, whereas the number of classes of the Polyangia and Actinobacteria affected the amounts of Pratylenchus spp. in both roots and soils. Soil organic matter, N, and Mn were the main factors that influenced the structure of the bacterial community. Correlations among rhizosphere microbiota, soil nematodes, and soil properties will be informative data in considering phytonematode management in a rice production system.

Plant endophytes: unveiling hidden applications toward agro-environment sustainability

Endophytic microbes are plant-associated microorganisms that reside in the interior tissue of plants without causing damage to the host plant. Endophytic microbes can boost the availability of nutrient for plant by using a variety of mechanisms such as fixing nitrogen, solubilizing phosphorus, potassium, and zinc, and producing siderophores, ammonia, hydrogen cyanide, and phytohormones that help plant for growth and protection against various abiotic and biotic stresses. The microbial endophytes have attained the mechanism of producing various hydrolytic enzymes such as cellulase, pectinase, xylanase, amylase, gelatinase, and bioactive compounds for plant growth promotion and protection. The efficient plant growth promoting endophytic microbes could be used as an alternative of chemical fertilizers for agro-environmental sustainability. Endophytic microbes belong to different phyla including Euryarchaeota, Ascomycota, Basidiomycota, Mucoromycota, Firmicutes, Proteobacteria, and Actinobacteria. The most pre-dominant group of bacteria belongs to Proteobacteria including α-, β-, γ-, and δ-Proteobacteria. The least diversity of the endophytic microbes have been revealed from Bacteroidetes, Deinococcus-Thermus, and Acidobacteria. Among reported genera, Achromobacter, Burkholderia, Bacillus, Enterobacter, Herbaspirillum, Pseudomonas, Pantoea, Rhizobium, and Streptomyces were dominant in most host plants. The present review deals with plant endophytic diversity, mechanisms of plant growth promotion, protection, and their role for agro-environmental sustainability. In the future, application of endophytic microbes have potential role in enhancement of crop productivity and maintaining the soil health in sustainable manner.

Endophytic Bacillus subtilis H17-16 effectively inhibits Phytophthora infestans, the pathogen of potato late blight, and its potential application

BACKGROUND

As a highly prevalent epidemic disease of potato, late blight caused by Phytophthora infestans poses a serious threat to potato yield and quality. At present, chemical fungicides are mainly used to control potato late blight, but long-term overuse of chemical fungicides may lead to environmental pollution and human health threats. Endophytes, natural resources for plant diseases control, can promote plant growth, enhance plant resistance, and secrete antifungal substances. Therefore, there is an urgent need to find some beneficial endophytes to control potato late blight.

RESULTS

We isolated a strain of Bacillus subtilis H17-16 from potato healthy roots. It can significantly inhibit mycelial growth, sporangia germination and the pathogenicity of Phytophthora infestans, induce the resistance of potato to late blight, and promote potato growth. In addition, H17-16 has the ability to produce protease, volatile compounds (VOCs) and form biofilms. After H17-16 treatment, most of the genes involved in metabolism, virulence and drug resistance of Phytophthora infestans were down-regulated significantly, and the genes related to ribosome biogenesis were mainly up-regulated. Moreover, field and postharvest application of H17-16 can effectively reduce the occurrence of potato late blight, and the combination of H17-16 with chitosan or chemical fungicides had a better effect than single H17-16.

CONCLUSION

Our results reveal that Bacillus subtilis H17-16 has great potential as a natural fungicide for controlling potato late blight, laying a theoretical basis for its development as a biological control agent. © 2023 Society of Chemical Industry.

Taxonomical, functional, and cytopathological characterization of Bacillus spp. from Lake Magadi, Kenya, against Rhizoctonia solani Kühn in Phaseolus vulgaris L

A decline in common bean production and the ineffectiveness of synthetic chemical products in managing plant pathogens has led to exploiting Kenyan soda lakes as an alternative search for biocontrol agents. This study aimed to identify phylogenetically Bacillus spp. from Lake Magadi and their antagonistic activity against Rhizoctonia solani under in vitro and in vivo conditions. The 16 S ribosomal RNA (rRNA) subunit sequences of six bacterial strains isolated from Lake Magadi showed diversity similar to the Bacillus genus; Bacillus velezensis, Bacillus subtilis, and Bacillus pumilus. In vitro, antagonism showed varied mycelium inhibition rates of fungi in the coculture method. Enzymatic assays showed the varied ability of isolates to produce phosphatase, pectinase, chitinase, protease, indole-3-acetic acid (IAA), and hydrogen cyanide (HCD). The in vivo assay showed M09 (B. velezensis) with the lowest root mortality and incidence of postemergence wilt. Pre-emergence wilt incidence was recorded as lowest in M10 (B. subtilis). Isolate M10 had the highest phenylalanine ammonia-lyase (PAL) for defense enzymes, while polyphenol oxidase (PPO) and peroxidase were recorded as highest in M09. For the phenolic content, M10 recorded the highest phenolic content. In conclusion, Lake Magadi harbors Bacillus spp, which can be used as a potential biocontrol of R. solani.

MALDI mass spectrometry-based identification of antifungal molecules from endophytic Bacillus strains with biocontrol potential of Lasiodiplodia theobromae, a grapevine trunk pathogen in Peru

Lasiodiplodia theobromae, a grapevine trunk pathogen, is becoming a significant threat to vineyards worldwide. In Peru, it is responsible for Botryosphaeria dieback in many grapevine-growing areas and it has spread rapidly due to its high transmissibility; hence, control measures are urgent. It is known that some endophytic bacteria are strong inhibitors of phytopathogens because they produce a wide range of antimicrobial molecules. However, studies of antimicrobial features from endophytic bacteria are limited to traditional confrontation methods. In this study, a MALDI mass spectrometry-based approach was performed to identify and characterize the antifungal molecules from Bacillus velezensis M1 and Bacillus amyloliquefaciens M2 grapevine endophytic strains. Solid medium antagonism assays were performed confronting B. velezensis M1 - L. theobromae and B. amyloliquefaciens M2 - L. theobromae for antifungal lipopeptides identification. By a MALDI TOF MS it was possible identify mass spectra for fengycin, iturin and surfactin protoned isoforms. Masses spectrums for mycobacillin and mycosubtilin were also identified. Using MALDI Imaging MS we were able to visualize and relate lipopeptides mass spectra of fengycin (1463.9 m/z) and mycobacillin (1529.6 m/z) in the interaction zone during confrontations. The presence of lipopeptides-synthesis genes was confirmed by PCR. Liquid medium antagonism assays were performed for a proteomic analysis during the confrontation of B. velezensis M1 - L. theobromae. Different peptide sequences corresponding to many antifungal proteins and enzymes were identified by MALDI TOF MS/MS. Oxalate decarboxylase bacisubin and flagellin, reported as antifungal proteins, were identified at 99 % identity through peptide mapping. MALDI mass spectrometry-based identification of antifungal molecules would allow the early selection of endophytic bacteria with antifungal features. This omics tool could lead to measures for prevention of grapevine diseases and other economically important crops in Peru.

Screening and Analysis of Antifungal Strains Bacillus subtilis JF-4 and B. amylum JF-5 for the Biological Control of Fusarium Wilt of Banana

PURPOSE

This study aimed to identify the antagonistic bacteria from the rhizosphere of healthy bananas that can effectively suppress the Fusarium wilt of banana, and to further investigate the inhibitory mechanism.

METHOD

The primary and secondary screening techniques were implemented using the double-plate and fermentation antagonism methods. The strain was identified based on physiological and biochemical tests, 16S rRNA gene sequencing, and specific gene amplification. The effects of crude extract on the protein content, lipid peroxidation, and pectinase activity of mycelia were determined from the identified isolates.

RESULTS

Two antagonistic bacteria, JF-4 and JF-5, were screened and initially identified as Bacillus subtilis (GenBank: OR125631) and B. amylum (GenBank: OR125632). The greenhouse experiment showed that the biological control efficiency of the two antagonists against the Fusarium wilt of banana was 48.3% and 40.3%, respectively. The catalase content produced by lipid peroxidation increased significantly after treatment with the crude extracts of JF-4 and JF-5 at concentrations of 0.69 μmol/L and 0.59 μmol/L, respectively. The protein and ergosterol content and pectinase activity decreased significantly. The two antagonistic bacteria might inhibit the growth of pathogens by enhancing lipid peroxidation and decreasing the synthesis of cell metabolites. Twenty compounds were identified by gas chromatography-mass spectrometry (GC-MS). B. subtilis JF-4 was further sequenced and assembled to obtain a complete circular chromosome genome of 681,804,824 bp. The genome consisted of a 4,310,825-bp-long scaffold.

CONCLUSION

The findings of this study may help elucidate the mechanism behind this biocontrol isolate.

Unlocking antagonistic potential of Bacillus amyloliquefaciens KRS005 to control gray mold

To establish a safe, efficient, and simple biocontrol measure for gray mold disease caused by Botrytis cinerea, the basic characteristics and antifungal activity of KRS005 were studied from multiple aspects including morphological observation, multilocus sequence analysis and typing (MLSA-MLST), physical-biochemical assays, broad-spectrum inhibitory activities, control efficiency of gray mold, and determination of plant immunity. The strain KRS005, identified as Bacillus amyloliquefaciens, demonstrated broad-spectrum inhibitory activities against various pathogenic fungi by dual confrontation culture assays, of which the inhibition rate of B. cinerea was up to 90.3%. Notably, through the evaluation of control efficiency, it was found that KRS005 fermentation broth could effectively control the occurrence of tobacco leaves gray mold by determining the lesion diameter and biomass of B. cinerea on tobacco leaves still had a high control effect after dilution of 100 folds. Meanwhile, KRS005 fermentation broth had no impact on the mesophyll tissue of tobacco leaves. Further studies showed that plant defense-related genes involved in reactive oxygen species (ROS), salicylic acid (SA), and jasmonic acid (JA)-related signal pathways were significantly upregulated when tobacco leaves were sprayed with KRS005 cell-free supernatant. In addition, KRS005 could inhibit cell membrane damage and increase the permeability of B. cinerea. Overall, KRS005, as a promising biocontrol agent, would likely serve as an alternative to chemical fungicides to control gray mold.

Microbial Biological Control of Fungi Associated with Grapevine Trunk Diseases: A Review of Strain Diversity, Modes of Action, and Advantages and Limits of Current Strategies

Grapevine trunk diseases (GTDs) are currently among the most important health challenges for viticulture in the world. Esca, Botryosphaeria dieback, and Eutypa dieback are the most current GTDs caused by fungi in mature vineyards. Their incidence has increased over the last two decades, mainly after the ban of sodium arsenate, carbendazim, and benomyl in the early 2000s. Since then, considerable efforts have been made to find alternative approaches to manage these diseases and limit their propagation. Biocontrol is a sustainable approach to fight against GTD-associated fungi and several microbiological control agents have been tested against at least one of the pathogens involved in these diseases. In this review, we provide an overview of the pathogens responsible, the various potential biocontrol microorganisms selected and used, and their origins, mechanisms of action, and efficiency in various experiments carried out in vitro, in greenhouses, and/or in vineyards. Lastly, we discuss the advantages and limitations of these approaches to protect grapevines against GTDs, as well as the future perspectives for their improvement.

Identification and characterization of biocontrol agent Lysinibacillus boronitolerans P42 against Cerrena unicolor that causes root rot of arecanut palm

The arecanut palm is one of the most important industrial crops in tropical area around the world. The root rot of arecanut palm, which is caused by Cerrena unicolor, has led to heavy economic losses and restricted greatly the development of arecanut industry, especially in Hainan province of China. The common use of chemical agents has worsened the problems of the emergence of resistant pathogens and the pollution of agricultural environment. This study aims to screen and identify a more effective and environment friendly biocontrol method for the prevention and treatment of root rot of arecanut palm. The mycelium growth rate is investigated to select antagonistic bacteria from tropical crop rotation fields which show improved resistance against soil-borne pathogens, and the strain P42 is revealed with the strongest antagonistic effects (82.18%). Based on 16 s rDNA sequence analysis, the strain P42 is identified as Lysinibacillus boronitolerans. In vitro antimicrobial activity shows that the strain P42 exhibits broad-spectrum antagonistic activity against a wide variety of tropical agricultural fungal pathogens, including Cerrena unicolor, Magnaporthe oryzea, Botryodiplodia theobromae, Neoscytalidium dimidiatum, Thanatephorus cucumeris, Fusarium oxysporum, and Botrytis cinerea Per.. The antagonistic activity of the culture of P42 is tolerant to common proteases, longer storage time, and temperature range of 40-121 °C; and is significantly influenced by alkaline (7-9) and acidic (1-2) pH, as well as by ultraviolet ray treatment for more than 30 min. The investigation on the antagonistic activity of the crude extract of fermentation filtrate indicates that the active compounds might be lipopeptides, polyketones, or proteins. To our knowledge, this is the first report of L. boronitolerans as potential bio-reagents for controlling root rot of arecanut palm caused by Cerrena unicolor.

Isolation and Screening of Antagonistic Endophytes against Phytophthora infestans and Preliminary Exploration on Anti-oomycete Mechanism of Bacillus velezensis 6-5

Phytophthora infestans, the notorious pathogen of potato late blight, leads to a severe decline in potato yields and even harvest failure. We isolated 201 endophytic isolates from healthy root tissues of potatoes, among which 41 showed strong antagonistic activity against P. infestans. Further, the tolerance to stress and the potential application against potato late blight of these antagonistic isolates were tested. Most of them were extremely tolerant to stresses such as acid-alkali, temperature, UV, salt, and heavy metal stress. However, some antagonistic isolates with excellent stress tolerance might be pathogenic to potatoes. Combining the screening results, a total of 14 endophytes had excellent comprehensive performance in all the tests. In this paper, the endophyte 6-5 was selected among them for the preliminary exploration of the anti-oomycete mechanism. Analysis of the 16S rDNA sequence revealed that 6-5 had a high homology to the corresponding sequence of Bacillus velezensis (99.72%) from the NCBI database. Endophyte 6-5 significantly inhibited the mycelial growth of P. infestans, with an inhibition rate of over 90% in vitro assays, and deformed the hyphal phenotype of P. infestans. In addition, endophyte 6-5 could secrete protease and cellulase, and produce antagonistic substances with high thermal stability, which might be helpful to its antagonistic activity against P. infestans. Furthermore, it was demonstrated that 6-5 had the ability to improve the resistance of potato tubers to late blight. In short, our study described the process of isolating and screening endophytes with antagonistic activity against P. infestans from potato roots, and further explored the potential of biocontrol candidate strain 6-5 in potato late blight control.

Breeding toward improved ecological plant-microbiome interactions

Domestication processes, amplified by breeding programs, have allowed the selection of more productive genotypes and more suitable crop lines capable of coping with the changing climate. Notwithstanding these advancements, the impact of plant breeding on the ecology of plant-microbiome interactions has not been adequately considered yet. This includes the possible exploitation of beneficial plant-microbe interactions to develop crops with improved performance and better adaptability to any environmental scenario. Here we discuss the exploitation of customized synthetic microbial communities in agricultural systems to develop more sustainable breeding strategies based on the implementation of multiple interactions between plants and their beneficial associated microorganisms.

Bacillus for Plant Growth Promotion and Stress Resilience: What Have We Learned?

The rhizosphere is a thin film of soil that surrounds plant roots and the primary location of nutrient uptake, and is where important physiological, chemical, and biological activities are occurring. Many microbes invade the rhizosphere and have the capacity to promote plant growth and health. Bacillus spp. is the most prominent plant growth promoting rhizobacteria due to its ability to form long-lived, stress-tolerant spores. Bacillus-plant interactions are driven by chemical languages constructed by a wide spectrum of metabolites and lead to enhanced plant growth and defenses. Thus, this review is a synthesis and a critical assessment of the current literature on the application of Bacillus spp. in agriculture, highlighting gaps that remain to be explored to improve and expand on the Bacillus-based biostimulants. Furthermore, we suggest that omics sciences, with a focus on metabolomics, offer unique opportunities to illuminate the chemical intercommunications between Bacillus and plants, to elucidate biochemical and molecular details on modes of action of Bacillus-based formulations, to generate more actionable insights on cellular and molecular events that explain the Bacillus-induced growth promotion and stress resilience in plants.

Biosynthetic Mechanisms of Secondary Metabolites Promoted by the Interaction Between Endophytes and Plant Hosts

Endophytes is a kind of microorganism resource with great potential medicinal value. The interactions between endophytes and host not only promote the growth and development of each other but also drive the biosynthesis of many new medicinal active substances. In this review, we summarized recent reports related to the interactions between endophytes and hosts, mainly regarding the research progress of endophytes affecting the growth and development of host plants, physiological stress and the synthesis of new compounds. Then, we also discussed the positive effects of multiomics analysis on the interactions between endophytes and their hosts, as well as the application and development prospects of metabolites synthesized by symbiotic interactions. This review may provide a reference for the further development and utilization of endophytes and the study of their interactions with their hosts.

Analysis of Conjunctival Sac Microbiome in Dry Eye Patients With and Without Sjögren's Syndrome

Purpose

To analyze the conjunctival sac microbial communities in patients with Sjögren's syndrome-associated dry eyes (SSDE) and non-Sjögren's syndrome-associated dry eyes (NSSDE), compared with normal controls (NC).

Methods

Conjunctival sac swab samples from 23 eyes of SSDE, 36 eyes of NSSDE, and 39 eyes of NC were collected. The V3–V4 region of the 16S ribosomal RNA (rRNA) gene high-throughput sequencing was performed on an Illumina MiSeq platform and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Alpha diversity was employed to analyze microbiome diversity through Chao1 and Shannon indexes. Beta diversity was demonstrated by the principal coordinates analysis (PCoA) and Partial Least Squares Discrimination Analysis (PLS-DA). The relative abundance was bioinformatically analyzed at the phylum and genus levels.

Results

The alpha diversity was lower in patients with dry eye disease (Shannon index: NC vs. SSDE: P = 0.020, NC vs. NSSDE: P = 0.029). The beta diversity showed divergent microbiome composition in different groups (NC vs. SSDE: P = 0.001, NC vs. NSSDE: P = 0.001, NSSDE vs. SSDE: P = 0.005). The top 5 abundant phyla were Firmicutes, Proteobacteria, Actinobacteriota, Bacteroidota, and Cyanobacteria in all three groups. The top five abundant genera included Acinetobacter, Staphylococcus, Bacillus, Corynebacterium, and Clostridium_sensu_stricto_1. The relative microbiome abundance was different between groups. The Firmicutes/Bacteroidetes (F/B) ratio was 6.42, 7.31, and 9.71 in the NC, NSSDE, and SSDE groups, respectively (NC vs. SSDE: P = 0.038, NC vs. NSSDE: P = 0.991, SSDE vs. NSSDE: P = 0.048).

Conclusion

The diversity of conjunctival sac microbiome in patients with NSSDE and SSDE was diminished compared with NC. The main microbiome at the phylum and genus level were similar between groups, but the relative abundance had variations. The Firmicutes/Bacteroidetes ratio was higher in the SSDE group.

Microbe-assisted crop improvement: a sustainable weapon to restore holobiont functionality and resilience

In the past years, breeding programs have been mainly addressed on pushing the commercial features, forgetting important traits, such as those related to environmental stress resilience, that are instead present in wild relatives. Among the traits neglected by breeding processes, the ability to recruit beneficial microorganisms that recently is receiving a growing attention due to its potentiality. In this context, this review will provide a spotlight on critical issues of the anthropocentric point of view that, until now, has characterized the selection of elite plant genotypes. Its effects on the plant-microbiome interactions, and the possibility to develop novel strategies mediated by the exploitation of beneficial root-microbe interactions, will be discussed. More sustainable microbial-assisted strategies might in fact foster the green revolution and the achievement of a more sustainable agriculture in a climatic change scenario.

Biocontrol of citrus bacterial canker caused by Xanthomonas citri subsp. citri by Bacillus velezensis

Microorganisms with biocontrol capabilities against plant pathogens are considered as one of the most promising approaches for healthy crop management. In this study, ethyl acetate extracts of 25 Bacillus strains were investigated for their antagonistic effect on Xanthomonas citri subsp. citri (Xcc), which causes the citrus bacterial canker (CBC) disease. Among them, 21 strains exerted antibacterial activity against wild-type Xcc strains. Based on the strength of the antibacterial activity, nine Bacillus strains were selected for 16S rRNA analysis. 16S rRNA sequence homology revealed that several strains were closely related to B. velezensis, where strains with no antibacterial activity grouped as the soil-associated community of B. amyloliquefaciens. B. velezensis Bv-21 exhibited the highest antibacterial activity against wild type and streptomycin resistant Xcc with inhibition zones of 22.91 ± 0.45 and 20.28 ± 0.53, respectively. Furthermore, B. velezensis Bv-21 strain was tested for biocontrol activity against a streptomycin-resistant XccM4 in detached susceptible citrus leaves. The strain reduced the incidence of CBC by 26.30% and pathogen density of XccM4 by 81.68% over control. The results of the study strongly suggest that B. velezensis can be used as an effective and eco-friendly biocontrol agent either by itself or as an active compound, against both, the wild-type and streptomycin-resistant Xcc.

In Vitro Inhibitory Activity of Cell-Free Supernatants of Lactobacillus Spp. and Bacillus Spp. Against Fusarium graminearum

In this study, the antifungal activity of cell-free supernatant (CFS) of Lactobacillus spp. (Lactobacillus plantarum CCM 1904; L81, Lactobacillus fermentum; 2I3, Lactobacilus reuteri; 2/6, L26;) and Bacillus spp. (Bacillus subtilis CCM 2794, Bacillus licheniformis CCM 2206) against two strains of Fusarium graminearum CCM F-683 and Fusarium graminearum CCM 8244 were investigated in vitro. All tested CFS of Lactobacillus spp. were able to inhibit the growth of both strains of Fusarium graminearum. The highest inhibitory effect (IE) (56.5 %) against F. graminearum CCM F-683 was observed for CFS Lactobacillus fermentum (2I3) at the minimum inhibitory concentration (MIC) (2.25 ± 0.56 mg.ml–1). CFS of Lactobacillus reuteri (2/6) showed the best IE (40.0 %) against F. graminearum CCM 8244 (2/6) at the MIC 1.25 mg.ml–1. However, no inhibitory effect of Bacillus subtilis and Bacillus licheniformis CFS against both strains of F. graminearum were observed, even at the highest tested concentration of 5.0 mg.ml–1.

Phytostimulation and biocontrol potential of Gram-positive endospore-forming Bacilli

The spore-forming Bacillus and Paenibacillus species represent the phyla of beneficial bacteria for application as agricultural inputs in form of effective phytostimulators, biofertilizers, and biocontrol agents. The members of the genera Bacillus and Paenibacillus isolated from several ecological habitats are been thoroughly dissected for their effective application in the development of sustainable and eco-friendly agriculture. Numerous Bacillus and Paenibacillus species are reported as plant growth-promoting bacteria influencing the health and productivity of the food crops. This review narrates the mechanisms utilized by these species to enhance bioavailability and/or facilitate the acquisition of nutrients by the host plant, modulate plant hormones, stimulate host defense and stress resistance mechanisms, exert antagonistic action against soil and airborne pathogens, and alleviate the plant health. The mechanisms employed by Bacillus and Paenibacillus are seldom mutually exclusive. The comprehensive and systematic exploration of the aforementioned mechanisms in conjunction with the field investigations may assist in the exploration and selection of an effective biofertilizer and a biocontrol agent. This review aims to gather and discuss the literature citing the applications of Bacillus and Paenibacillus in the management of sustainable agriculture.

Harvesting the complex pathways of antibiotic production and resistance of soil bacilli for optimizing plant microbiome

A sustainable future increasing depends on our capacity to utilize beneficial plant microbiomes to meet our growing needs. Plant microbiome symbiosis is a hallmark of the beneficial interactions between bacteria and their host. Specifically, colonization of plant roots by biocontrol agents and plant growth-promoting bacteria can play an important role in maintaining the optimal rhizosphere environment, supporting plant growth and promoting its fitness. Rhizosphere communities confer immunity against a wide range of foliar diseases by secreting antibiotics and activating plant defences. At the same time, the rhizosphere is a highly competitive niche, with multiple microbial species competing for space and resources, engaged in an arms race involving the production of a vast array of antibiotics and utilization of a variety of antibiotic resistance mechanisms. Therefore, elucidating the mechanisms that govern antibiotic production and resistance in the rhizosphere is of great significance for designing beneficial communities with enhanced biocontrol properties. In this review, we used Bacillus subtilis and B. amyloliquefaciens as models to investigate the genetics of antibiosis and the potential for its translation of into improved plant microbiome performance.

Genome Mining and Evaluation of the Biocontrol Potential of Pseudomonas fluorescens BRZ63, a New Endophyte of Oilseed Rape (Brassica napus L.) against Fungal Pathogens

Endophytic bacteria hold tremendous potential for use as biocontrol agents. Our study aimed to investigate the biocontrol activity of Pseudomonas fluorescens BRZ63, a new endophyte of oilseed rape (Brassica napus L.) against Rhizoctonia solani W70, Colletotrichum dematium K, Sclerotinia sclerotiorum K2291, and Fusarium avenaceum. In addition, features crucial for biocontrol, plant growth promotion, and colonization were assessed and linked with the genome sequences. The in vitro tests showed that BRZ63 significantly inhibited the mycelium growth of all tested pathogens and stimulated germination and growth of oilseed rape seedlings treated with fungal pathogens. The BRZ63 strain can benefit plants by producing biosurfactants, siderophores, indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and ammonia as well as phosphate solubilization. The abilities of exopolysaccharide production, autoaggregation, and biofilm formation additionally underline its potential to plant colonization and hence biocontrol. The effective colonization properties of the BRZ63 strain were confirmed by microscopy observations of EGFP-expressing cells colonizing the root surface and epidermal cells of Arabidopsis thaliana Col-0. Genome mining identified many genes related to the biocontrol process, such as transporters, siderophores, and other secondary metabolites. All analyses revealed that the BRZ63 strain is an excellent endophytic candidate for biocontrol of various plant pathogens and plant growth promotion.

Draft Genome Sequence of Bacillus licheniformis Strain UASWS1606, a Plant Biostimulant for Agriculture

Bacillus licheniformis is a well-known industrial bacterium. New strains show interesting properties of biostimulants and biological control agents for agriculture. Here, we report the draft genome sequence, obtained with an Illumina MiniSeq system, of strain UASWS1606 of the bacterium Bacillus licheniformis, which is being developed as an agricultural biostimulant.

Bacillus licheniformis is a well-known industrial bacterium. New strains show interesting properties of biostimulants and biological control agents for agriculture. Here, we report the draft genome sequence, obtained with an Illumina MiniSeq system, of strain UASWS1606 of the bacterium Bacillus licheniformis, which is being developed as an agricultural biostimulant.

The invisible life inside plants: Deciphering the riddles of endophytic bacterial diversity

Endophytic bacteria often promote plant growth and protect their host plant against pathogens, herbivores, and abiotic stresses including drought, increased salinity or pollution. Current agricultural practices are being challenged in terms of climate change and the ever-increasing demand for food. Therefore, the rational exploitation of bacterial endophytes to increase the productivity and resistance of crops appears to be very promising. However, the efficient and larger-scale use of bacterial endophytes for more effective and sustainable agriculture is hindered by very little knowledge on molecular aspects of plant-endophyte interactions and mechanisms driving bacterial communities in planta. In addition, since most of the information on bacterial endophytes has been obtained through culture-dependent techniques, endophytic bacterial diversity and its full biotechnological potential still remain highly unexplored. In this study, we discuss the diversity and role of endophytic populations as well as complex interactions that the endophytes have with the plant and vice versa, including the interactions leading to plant colonization. A description of biotic and abiotic factors influencing endophytic bacterial communities is provided, along with a summary of different methodologies suitable for determining the diversity of bacterial endophytes, mechanisms governing the assembly and structure of bacterial communities in the endosphere, and potential biotechnological applications of endophytes in the future.

Plant resistance and leaf chemical characteristic jointly shape phyllosphere bacterial community

Phyllosphere bacteria have an important role in plant growth and resistance to pathogen infection and are partially influenced by plant genotype and leaf environment. How plant resistance to pathogens and leaf chemical characteristics shape the phyllosphere bacterial communities is unclear. In this study, the phyllosphere bacterial communities of maize hybrids with various resistance to Setosphaeria turcica were compared using the high-throughput sequencing and large-scale culturing methods. The results showed that Shannon and Simpson indices of phyllosphere bacterial communities were markedly higher in the highly resistant hybrid (HR) compared with the susceptible one. Hierarchical clustering analysis, unweighted UniFrac principal component analysis (PCoA) and the analysis of similarities (ANOSIM) demonstrated that the phyllosphere bacterial communities were significantly distinct between resistant and susceptible hybrids. The redundancy analysis (RDA) demonstrated that leaf chemical characteristics, including nitrogen and phosphorus concentration, and disease resistance play an important role in shaping the phyllosphere bacterial community. Linear discriminant effect size (LEfSe) analysis indicated that Bacillus, Pseudomonas and Tumebacillus were the biomarker species in the phyllosphere of HR. Biocontrol bacteria against S. turcica (such as Pseudomonas and Bacillus) were isolated from the phyllosphere of HR by large-scale culturing. The work contributes to understanding of the phyllosphere bacterial community assembly and provides a new clue to screening for strong biocontrol bacteria from HR and to facilitating future breeding efforts for enhancing disease resistance.

Bacillus strain selection with plant growth-promoting mechanisms as potential elicitors of systemic resistance to gray mold in pepper plants

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Bacillus licheniformis induced resistance against gray mold in pepper plants.

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Bacillus licheniformis and Bacillus pumilus inhibited the growth of Botrytis cinerea and Fusarium solani.

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Plant growth promoting mechanisms were confirmed by isolated Bacillus strains.

Certain soil bacteria produce beneficial effects on the growth and health of plants; hence, their use is steadily increasing. Five strains of Bacillus with plant growth-promoting potential were selected in this study, which produced indole-3-acetic acid levels below 50 µg.mL⁻¹. On the other hand, while only strains M8 and M15 dissolved phosphorus, the latter was the only strain that did not produce siderophores. Only strains M8 and M16 significantly inhibited the in vitro growth of Botrytis cinerea and Fusarium solani phytopathogens, whose inhibition ranges fluctuated between 60% and 63% for strains M8 and M16 against B. cinerea and between 40% and 53% for strains M8 and M16 against F. solani. Based on these results, the need to implement resistance induction against gray mold on pepper plants was determined using strains M8 and M16. In this case, strain M16 inhibited the propagation of the necrotic spot by approximately 70%, whereas strain M8 significantly reduced the superoxide dismutase activity in systemic leaves, which substantially increased in plants inoculated with strain M8 and infected with the pathogen. Accordingly, the use of native rhizobacteria may entail biotechnological progress for the integrated management of crops in agriculture industry.

Endophytic microbial assemblage in grapevine

The plant vascular system has remained an underexplored niche despite its potential for hosting beneficial microbes. The aim of this work was to determine the origin of the microbial endophytes inhabiting grapevine. We focused on a single commercial vineyard in California over a two-year period and used an amplicon metagenomics approach to profile the bacterial (16S–V4) and fungal (ITS) communities of the microbiome across a continuum of six grapevine compartments: bulk soil, rhizosphere, root, cordon, cane and sap. Our data supported that roots are a bottleneck to microbial richness and that they are mostly colonized with soilborne microbes, including plant growth-promoting bacteria recruited by the host, but also saprophytic and pathogenic fungal invaders. A core group of taxa was identified throughout the vine; however, there was clear partitioning of the microbiome with niche adaptation of distinct taxonomic groups. Above- and belowground plant tissues displayed distinct microbial fingerprints and were intermixed in a limited capacity mostly by way of the plant sap. We discuss how cultural practices and human contact may shape the endosphere microbiome and identify potential channels for transmission of its residents.

Remediation mechanism of endophytic fungus Phomopsis liquidambaris on phenanthrene in vivo

Phenanthrene can easily be absorbed into the plant from the soil and cannot be effectively degraded in it. Thus, it is greatly hazardous for food safety and human health. In our study, the biodegradability and remediation mechanism of endophytic fungus Phomopsis liquidambaris on phenanthrene in vivo of rice (Oryza sativa L.) was detected. The results showed that the fungus could successfully establish a symbiotic relationship with rice, thus had the potential to degrade phenanthrene absorbed into the plant. Changes of phenanthrene-degrading genes of fungus in the combined system were consistent with the trends of their corresponding enzymatic activities, and the phenanthrene-degrading enzyme activities and gene expression levels in roots of rice were higher than those in the shoot. Moreover, the combined system can enhance bioremediation by increasing root viability, chlorophyll content, and energy supply. The combined system had also significantly increased the PPO activity and SOD activity in shoot compared with the control treatment, while decreased the content of MDA when remediation in vivo. The study on the degradation mechanism of the combined system will help us to increase the practical application potential of endophyte to effectively repair contamination absorbed into plant seedlings.

Investigation and Application of Bacillus licheniformis Volatile Compounds for the Biological Control of Toxigenic Aspergillus and Penicillium spp

The present study was designed to investigate the antagonistic activity of Bacillus licheniformis BL350-2 against mycotoxigenic strains of Aspergillus and Penicillium. In vitro coincubation for 5 days indicated Aspergillus westerdijkiae BA1 as the most sensitive strain, with a growth inhibition of 62%, followed by A. carbonarius MG7 (60%), Penicillium verrucosum MC12 (53%), A. niger MC05 (50%), A. flavus CM5 (49%), A. parasiticus SB01 (47%), and A. ochraceus MD1 (44%). Likewise, the majority of the tested strains on exposure to bacterial volatiles showed complete inhibition of mycotoxin synthesis. In vivo assays on maize ears resulted in 88% reduction in A. flavus CM5 growth and complete inhibition of fungal sporulation and aflatoxin accumulation. The GC-MS-based volatile profile showed 3-methyl-1-butanol as the most abundant compound. The findings of the present study advocate that B. licheniformis BL350-2 is suitable as a biocontrol agent against mycotoxigenic fungi, at least during storage of cereal grains.

The Role of the Endophytic Microbiome in the Grapevine Response to Environmental Triggers

Endophytism within Vitis represents a topic of critical relevance due to the multiple standpoints from which it can be approached and considered. From the biological and botanical perspectives, the interaction between microorganisms and perennial woody plants falls within the category of stable relationships from which the plants can benefit in multiple ways. The life cycle of the host ensures persistence in all seasons, repeated chances of contact, and consequent microbiota accumulation over time, leading to potentially high diversity compared with that of herbaceous short-lived plants. Furthermore, grapevines are agriculturally exploited, highly selected germplasms where a profound man-driven footprint has indirectly and unconsciously shaped the inner microbiota through centuries of cultivation and breeding. Moreover, since endophyte metabolism can contribute to that of the plant host and its fruits' biochemical composition, the nature of grapevine endophytic taxa identities, ecological attitudes, potential toxicity, and clinical relevance are aspects worthy of a thorough investigation. Can endophytic taxa efficiently defend grapevines by acting against pests or confer enough fitness to the plants to endure attacks? What are the underlying mechanisms that translate into this or other advantages in the hosting plant? Can endophytes partially redirect plant metabolism, and to what extent do they act by releasing active products? Is the inner microbial colonization necessary priming for a cascade of actions? Are there defined environmental conditions that can trigger the unleashing of key microbial phenotypes? What is the environmental role in providing the ground biodiversity by which the plant can recruit microsymbionts? How much and by what practices and strategies can these symbioses be managed, applied, and directed to achieve the goal of a better sustainable viticulture? By thoroughly reviewing the available literature in the field and critically examining the data and perspectives, the above issues are discussed.

Screening of the High-Rhizosphere Competent Limoniastrum monopetalum' Culturable Endophyte Microbiota Allows the Recovery of Multifaceted and Versatile Biocontrol Agents

Halophyte Limoniastrum monopetalum, an evergreen shrub inhabiting the Mediterranean region, has well-documented phytoremediation potential for metal removal from polluted sites. It is also considered to be a medicinal halophyte with potent activity against plant pathogens. Therefore, L. monopetalum may be a suitable candidate for isolating endophytic microbiota members that provide plant growth promotion (PGP) and resistance to abiotic stresses. Selected for biocontrol abilities, these endophytes may represent multifaceted and versatile biocontrol agents, combining pathogen biocontrol in addition to PGP and plant protection against abiotic stresses. In this study 117 root culturable bacterial endophytes, including Gram-positive (Bacillus and Brevibacillus), Gram-negative (Proteus, Providencia, Serratia, Pantoea, Klebsiella, Enterobacter and Pectobacterium) and actinomycete Nocardiopsis genera have been recovered from L. monopetalum. The collection exhibited high levels of biocontrol abilities against bacterial (Agrobacterium tumefaciens MAT2 and Pectobacterium carotovorum MAT3) and fungal (Alternaria alternata XSZJY-1, Rhizoctonia bataticola MAT1 and Fusarium oxysporum f. sp. radicis lycopersici FORL) pathogens. Several bacteria also showed PGP capacity and resistance to antibiotics and metals. A highly promising candidate Bacillus licheniformis LMRE 36 with high PGP, biocontrol, metal and antibiotic, resistance was subsequently tested in planta (potato and olive trees) for biocontrol of a collection of 14 highly damaging Fusarium species. LMRE 36 proved very effective against the collection in both species and against an emerging Fusarium sp. threatening olive trees culture in nurseries. These findings provide a demonstration of our pyramiding strategy. Our strategy was effective in combining desirable traits in biocontrol agents towards broad-spectrum resistance against pathogens and protection of crops from abiotic stresses. Stacking multiple desirable traits into a single biocontrol agent is achieved by first, careful selection of a host for endophytic microbiota recovery; second, stringent in vitro selection of candidates from the collection; and third, application of the selected biocontrol agents in planta experiments. That pyramiding strategy could be successfully used to mitigate effects of diverse biotic and abiotic stresses on plant growth and productivity. It is anticipated that the strategy will provide a new generation of biocontrol agents by targeting the microbiota of plants in hostile environments.

Temporal Dynamics of the Sap Microbiome of Grapevine Under High Pierce's Disease Pressure

Grapevine is a pillar of the California state economy and agricultural identity. This study provides a comprehensive culture-independent microbiome analysis from the sap of grapevine overtime and in a context of a vascular disease. The vascular system plays a key role by transporting nutrient, water and signals throughout the plant. The negative pressure in the xylem conduits, and low oxygen and nutrient content of its sap make it a unique and underexplored microbial environment. We hypothesized that grapevine hosts in its sap, microbes that have a beneficial impact on plant health by protecting against pathogen attack and supporting key biological processes. To address this hypothesis, we chose a vineyard under high Pierce's disease (PD). PD is caused by the xylem-dwelling pathogenic bacterium Xylella fastidiosa. We selected ten grapevines within this vineyard with a range of disease phenotypes, and monitored them over 2 growing seasons. We sampled each vines at key phenological stages (bloom, veraison, and post-harvest) and used an amplicon metagenomics approach to profile the bacterial (16S -V4) and fungal (ITS) communities of the sap. We identified a core microbiome of the sap composed of seven bacterial (Streptococcus, Micrococcus, Pseudomonas, Bacteroides, Massilia, Acinetobacter and Bacillus) and five fungal (Cladosporium, Mycosphaerella, Alternaria, Aureobasidium, and Filobasidium) taxa that were present throughout the growing season. Overall, the sap microbial makeup collected from canes was more similar to the root microbial profile. Alpha diversity metrics indicated a microbial enrichment at bloom and in vines with moderate PD severity suggesting a host-driven microbial response to environmental cues. Beta diversity metrics demonstrated that disease condition and plant phenology impacted microbial community profiles. Our study identified several potential taxonomic targets with antimicrobial and plant growth promoting capabilities that inhabit the grapevine sap and that should be further tested as potential biological control or biofertilizer agents.