Genomic and Functional Characterization of the Endophytic Bacillus subtilis 7PJ-16 Strain, a Potential Biocontrol Agent of Mulberry Fruit Sclerotiniose

Structural characterization and high-efficiency prebiotic activity of the polysaccharide from Tremella aurantialba endophytic bacteria

Herein, the low-molecular-weight heteropolysaccharide (designated as TABP), with a weight-average Mw of 5408 Da, was produced by the endophytic bacterium Bacillus sp. TAB, which was initially isolated from the fruiting bodies of the wild Tremella aurantialba. A relatively high TABP accumulation was obtained and enhanced to 6.94 g/L in 5 L fed-batch fermentation by high-density cultivation. Monosaccharide composition analysis showed that the TABP comprised arabinose, glucosamine, galactose, glucose, and mannose with a molar ratio of 0.073: 0.145: 0.406: 0.182: 0.195, respectively. Methylation and NMR analyses indicated that TABP contained 1,4-linked β-d-Galp and 1,4-linked β-d-Manp pyranosyl backbone, extensively substituted at the side chains to form a complex structure. Prebiotic potential analysis exhibited significant growth-promoting effects for various lactic acid bacteria by more than 90 %. Overall, this study initially provides valuable insights into the endophytic exopolysaccharides from T. aurantialba and their biological activity, which provides prospective sources of prebiotics for functional foods and aids in understanding the endophytes symbiosis mechanism in edible mushrooms.

Bacillus species as tools for biocontrol of plant diseases: A meta-analysis of twenty-two years of research, 2000-2021

The traditional way of dealing with plant diseases has been the use of chemical products, but these harm the environment and are incompatible with the global effort for sustainable development. The use of Bacillus and related species in the biological control of plant diseases is a trend in green agriculture. Many studies report the positive effect of these bacteria, but a synthesis is still necessary. So, the objective of this work is to perform a meta-analysis of Bacillus biocontrol potential and identify factors that drive its efficacy. Data were compiled from articles published in journals listed in two of the main scientific databases between 2000 and 2021. Among 6159 articles retrieved, 399 research papers met the inclusion criteria for a systematic review. Overall, Bacilli biocontrol agents reduced disease by 60% compared to control groups. Furthermore, experimental tests with higher concentrations show a strong protective effect, unlike low and single concentration essays. Biocontrol efficacy also increased when used as a protective inoculation rather than therapeutic inoculation. Inoculation directly in the fruit has a greater effect than soil drenching. The size of the effect of Bacillus-based commercial products is lower than the newly tested strains. The findings presented in this study confirm the power of Bacillus-based bioinoculants and provide valuable guidance for practitioners, researchers, and policymakers seeking effective and sustainable solutions in plant disease management.

Survival strategies of Bacillus spp. in saline soils: Key factors to promote plant growth and health

Soil salinity is one of the most important abiotic factors that affects agricultural production worldwide. Because of saline stress, plants face physiological changes that have negative impacts on the various stages of their development, so the employment of plant growth-promoting bacteria (PGPB) is one effective means to reduce such toxic effects. Bacteria of the Bacillus genus are excellent PGPB and have been extensively studied, but what traits makes them so extraordinary to adapt and survive under harsh situations? In this work we review the Bacillus' innate abilities to survive in saline stressful soils, such as the production osmoprotectant compounds, antioxidant enzymes, exopolysaccharides, and the modification of their membrane lipids. Other survival abilities are also discussed, such as sporulation or a reduced growth state under the scope of a functional interaction in the rhizosphere. Thus, the most recent evidence shows that these saline adaptive activities are important in plant-associated bacteria to potentially protect, direct and indirect plant growth-stimulating activities. Additionally, recent advances on the mechanisms used by Bacillus spp. to improve the growth of plants under saline stress are addressed, including genomic and transcriptomic explorations. Finally, characterization and selection of Bacillus strains with efficient survival strategies are key factors in ameliorating saline problems in agricultural production.

Bacillus sp. as a microbial cell factory: Advancements and future prospects

Bacillus sp. is one of the most distinctive gram-positive bacteria, able to grow efficiently using cheap carbon sources and secrete a variety of useful substances, which are widely used in food, pharmaceutical, agricultural and environmental industries. At the same time, Bacillus sp. is also recognized as a safe genus with a relatively clear genetic background, which is conducive to the industrial production of target metabolites. In this review, we discuss the reasons why Bacillus sp. has been so extensively studied and summarize its advances in systems and synthetic biology, engineering strategies to improve microbial cell properties, and industrial applications in several metabolic engineering applications. Finally, we present the current challenges and possible solutions to provide a reliable basis for Bacillus sp. as a microbial cell factory.

Towards further understanding the applications of endophytes: enriched source of bioactive compounds and bio factories for nanoparticles

The most significant issues that humans face today include a growing population, an altering climate, an growing reliance on pesticides, the appearance of novel infectious agents, and an accumulation of industrial waste. The production of agricultural goods has also been subject to a great number of significant shifts, often known as agricultural revolutions, which have been influenced by the progression of civilization, technology, and general human advancement. Sustainable measures that can be applied in agriculture, the environment, medicine, and industry are needed to lessen the harmful effects of the aforementioned problems. Endophytes, which might be bacterial or fungal, could be a successful solution. They protect plants and promote growth by producing phytohormones and by providing biotic and abiotic stress tolerance. Endophytes produce the diverse type of bioactive compounds such as alkaloids, saponins, flavonoids, tannins, terpenoids, quinones, chinones, phenolic acids etc. and are known for various therapeutic advantages such as anticancer, antitumor, antidiabetic, antifungal, antiviral, antimicrobial, antimalarial, antioxidant activity. Proteases, pectinases, amylases, cellulases, xylanases, laccases, lipases, and other types of enzymes that are vital for many different industries can also be produced by endophytes. Due to the presence of all these bioactive compounds in endophytes, they have preferred sources for the green synthesis of nanoparticles. This review aims to comprehend the contributions and uses of endophytes in agriculture, medicinal, industrial sectors and bio-nanotechnology with their mechanism of action.

Comparative Study of Three Biological Control Agents and Two Conventional Fungicides against Coriander Damping-off and Root Rot Caused by Rhizoctonia solani

The in vitro and in vivo efficacy of three biocontrol agents, Trichoderma viride, Pseudomonas fluorescence, and Bacillus subtilis, were tested against Rhizoctonia solani (AG-4) infection compared to two conventional fungicides (Rizolex-T 50%wettable powder and Amistar 25%). Antifungal enzyme activity was assayed in the culture filtrate of the biocontrol agents. The impact of the tested biocontrol agents on the induction of the coriander immune system was investigated against R. solani by assessing the resistance-related enzymes and compounds in biocontrol agent-treated plants compared with the control. The obtained results revealed that all tested biocontrol agents significantly reduced the linear growth of R. solani, and T. viride recorded the highest inhibition percentage. This could be linked to the ability of T. viride to produce higher activities of antimicrobial enzymes, i.e., cellulase, chitinase, and protease, compared to P. fluorescence and B. subtilis. Applying the tested biocontrol agents significantly alleviated pre- and post-emergence damping-off and root rot/wilt diseases of infected coriander compared with untreated plants. The tested biocontrol agents exhibited significantly higher germination percentage and vigor index of the coriander than the tested fungicides. The tested biocontrol agents significantly minimized the reduction of photosynthetic pigments induced by R. solani. In addition, the results showed a significant increase in enzymes/molecules (i.e., phenylalanine, catalase, peroxidase, catalase, superoxide dismutase, phenylalanine ammonia-lyase, phenolics, ascorbic acids, and salicylic acid) involved directly and indirectly in coriander resistance to R. solani. The principal component analysis of the recorded data recommended the role of the high accumulation of oxidative parameters (hydrogen peroxide and lipid peroxidation) and the inhibition of phenolic compounds in the downregulation of coriander resistance against R. solani. The heatmap analysis results revealed that biocontrol agents, especially Trichoderma, enhanced the resistance against R. solani via the stimulation of salicylic acid, phenolics, and antioxidant enzymes. Overall, the data recommended the efficacy of biocontrol agents, especially T. viride, against R. solani infecting coriander plants, which could be an efficient and a safer alternative to conventional fungicides.

Plant-Endophyte Interaction during Biotic Stress Management

Plants interact with diverse microbial communities and share complex relationships with each other. The intimate association between microbes and their host mutually benefit each other and provide stability against various biotic and abiotic stresses to plants. Endophytes are heterogeneous groups of microbes that live inside the host tissue without showing any apparent sign of infection. However, their functional attributes such as nutrient acquisition, phytohormone modulation, synthesis of bioactive compounds, and antioxidant enzymes of endophytes are similar to the other rhizospheric microorganisms. Nevertheless, their higher colonization efficacy and stability against abiotic stress make them superior to other microorganisms. In recent studies, the potential role of endophytes in bioprospecting has been broadly reported. However, the molecular aspect of host–endophyte interactions is still unclear. In this study, we have briefly discussed the endophyte biology, colonization efficacy and diversity pattern of endophytes. In addition, it also summarizes the molecular aspect of plant–endophyte interaction in biotic stress management.

Evaluation and Genome Analysis of Bacillus subtilis YB-04 as a Potential Biocontrol Agent Against Fusarium Wilt and Growth Promotion Agent of Cucumber

Cucumber wilt caused by Fusarium oxysporum f.sp. cucumerinum (Foc) is a highly destructive disease that leads to reduced yield in cucumbers. In this study, strain YB-04 was isolated from wheat straw and identified as Bacillus subtilis. It displayed strong antagonistic activity against F. oxysporum f.sp. cucumerinum in dual culture and exhibited significant biocontrol of cucumber Fusarium wilt with a higher control effect than those of previously reported Bacillus strains and displayed pronounced growth promotion of cucumber seedlings. B. subtilis YB-04 could secrete extracellular protease, amylase, cellulose, and β-1,3-glucanase and be able to produce siderophores and indole acetic acid. Inoculation with B. subtilis YB-04 or Foc increased cucumber defense-related enzyme activities for PPO, SOD, CAT, PAL, and LOX. However, the greatest increase was with the combination of B. subtilis YB-04 and Foc. Sequencing the genome of B. subtilis YB-04 showed that it had genes for the biosynthesis of various secondary metabolites, carbohydrate-active enzymes, and assimilation of nitrogen, phosphorous, and potassium. B. subtilis YB-04 appears to be a promising biological control agent against the Fusarium wilt of cucumber and promotes cucumber growth by genomic, physiological, and phenotypic analysis.

In Vitro Study of Biocontrol Potential of Rhizospheric Pseudomonas aeruginosa against Pathogenic Fungi of Saffron (Crocus sativus L.)

Plant rhizosphere soil contains a large number of plant-growth promoting rhizobacteria, which can not only resist the invasion of pathogenic microorganisms and protect plants from damage, but also promote the growth and development of plants. In this study, Pseudomonas aeruginosa strain YY322, isolated and screened from the rhizosphere soil of saffron (Crocus sativus L.), was found through a plate confrontation experiment to show highly effectual and obvious antagonistic activity against the pathogens of saffron, including Fusarium oxysporum, Fusarium solani, Penicillium citreosulfuratum, Penicillium citrinum and Stromatinia gladioli. In addition, the volatile organic compounds of strain YY322 had great antagonistic activity against these pathogens. Observation under a scanning electron microscope and transmission electron microscope reflected that strain YY322 had a significant effect on the hyphae and conidia of F. oxysporum and F. solani. Through the detection of degrading enzymes, it was found that P. aeruginosa can secrete protease and glucanase. The plant growth promoting performance was evaluated, finding that strain YY322 had the functions of dissolving phosphorus, fixing nitrogen, producing siderophore and producing NH3. In addition, whole genome sequencing analysis indicated that the YY322 genome is comprised of a 6,382,345-bp circular chromosome, containing 5809 protein-coding genes and 151 RNA genes. The P. aeruginosa YY322 genome encodes genes related to phenazine (phzABDEFGIMRS), hydrogen cyanide(HCN) (hcnABC), surfactin (srfAA), salicylate (pchA), biofilm formation (flgBCDEFGHIJKL, motAB, efp, hfq), and colonization (minCDE, yjbB, lysC). These results collectively indicated the role of P. aeruginosa YY322 in plant growth enhancement and biocontrol mechanisms. All in all, this study provides a theoretical basis for P. aeruginosa as the PGPR of saffron, paving the way for the subsequent development and utilization of microbial fertilizer.

Seasonal Characterization of the Endophytic Fungal Microbiome of Mulberry (Morus spp.) Cultivars Resistant and Susceptible to Sclerotiniosis

The endophytic microbiome is thought to play an important role in promoting plant growth and health. Using culture-independent and culture-dependent protocols, this study characterized the seasonal shifts in the endophytic fungal microbiota of four mulberry (Morus L.) cultivars having different levels of resistance to mulberry fruit sclerotiniosis. Core endophytes can be obtained by two approaches, and they were divided into two clusters by season. Spring samples harbored higher operational taxonomic units (OTUs) and α-diversity, while autumn samples had more sequences or isolates of the fungal class Dothideomycetes with the representative orders Capnodiales and Pleosporales. While comparing different mulberry cultivars, we found that the total number of OTUs in susceptible cultivars was higher than that of resistant cultivars, and Cladosporium sp. were observed in all. Notably, the causal agent of fruit sclerotiniosis (Scleromitrula shiraiana) was only detected in susceptible cultivars. Collectively, our work elucidated significant variations in the mulberry endophytic microbiome, mainly because of seasonal shifts, and the fact that the host cultivars and mulberry endophytic fungal community appeared to have a certain connection with the resistance level of mulberry fruit to sclerotiniosis. These results provided valuable information on the isolation and culturing of mulberry endophytes that could be applied to improve mulberry fruit production and health.

Genome Mining of Three Plant Growth-Promoting Bacillus Species from Maize Rhizosphere

Bacillus species genomes are rich in plant growth-promoting genetic elements. Bacillus subtilis and Bacillus velezensis are important plant growth promoters; hence, to further improve their abilities, the genetic elements responsible for these traits were characterized and reported. Genetic elements reported include those of auxin, nitrogen fixation, siderophore production, iron acquisition, volatile organic compounds, and antibiotics. Furthermore, the presence of phages and antibiotic-resistant genes in the genomes are reported. Pan-genome analysis was conducted using ten Bacillus species. From the analysis, pan-genome of Bacillus subtilis and Bacillus velezensis are still open. Ultimately, this study brings an insight into the genetic components of the plant growth-promoting abilities of these strains and shows their potential biotechnological applications in agriculture and other relevant sectors.

Endophytic Bacillus subtilis P10 from Prunus cerasifera as a biocontrol agent against tomato Verticillium wilt

Endophytic bacteria serve key roles in the maintenance of plant health and growth. Few studies to date, however, have explored the antagonistic and plant growth-promoting (PGP) properties of Prunus cerasifera endophytes. To that end, we isolated endophytic bacteria from P. cerasifera tissue samples and used a dual culture plate assay to screen these microbes for antagonistic activity against Verticillium dahliae, Botryosphaeria dothidea, Fusarium oxysporum, F. graminearum, and F. moniliforme. Of the 36 strains of isolated bacteria, four (strains P1, P10, P16, and P20) exhibited antagonistic effects against all five model pathogens, and the P10 strain exhibited the strongest antagonistic to five pathogens. This P10 strain was then characterized in-depth via phenotypic assessments, physiological analyses, and 16s rDNA sequencing, revealing it to be a strain of Bacillus subtilis. Application of a P10 cell suspension (1×108 CFU/mL) significantly enhanced the seed germination and seedling growth of tomato in a greenhouse setting. This P10 strain further significantly suppressed tomato Verticillium wilt with much lower disease incidence and disease index scores being observed following P10 treatment relative to untreated plants in pot-based experiments. Tomato plants that had been treated with strain P10 also enhanced defense-related enzymes, peroxidase, superoxide dismutase, and catalase activity upon V. dahliae challenge relative to plants that had not been treated with this endophytic bacterium. The results revealed that the P10 bacterial strain has potential value as a biocontrol agent for use in the prevention of tomato Verticillium wilt.

Profiling of Metabolites of Bacillus spp. and Their Application in Sustainable Plant Growth Promotion and Biocontrol

Bacillus spp. are well-characterized as efficient bioinoculants for sustainable plant growth promotion and biocontrol of phytopathogens. Members of this spp. exhibit the multifaceted beneficial traits that are involved in plant nutrition and antimicrobial activities against phytopathogens. Keeping in view their diverse potential, this study targeted the detailed characterization of three root-colonizing Bacillus strains namely B. amyloliquefaciens, B. subtilis, and B. tequilensis, characterized based on 16S rRNA sequencing homology. The strains exhibited better plant growth promotion and potent broad-spectrum antifungal activities and exerted 43–86% in-vitro inhibition of growth of eight fungal pathogens. All strains produced indole acetic acid (IAA) in the range of 0.067–0.147 μM and were positive for the production of extracellular enzymes such as cellulase, lipase, and protease. Ultra-performance Liquid Chromatography-Electrospray Ionization-Mass Spectrometry (UPLC-ESI-MS/MS) analysis revealed the production of antifungal metabolites (AFMs) such as surfactins, iturins, fengycins, macrolactins, bacillomycin-D, and catechol-based siderophore bacillibactin which were further confirmed by amplifying the genes involved in the biosynthesis of these antimicrobial lipopeptides. When compared for the amounts of different cyclic-peptides produced by three Bacillus strains, B. amyloliquefaciens SB-1 showed the most noticeable amounts of all the antifungal compounds. Plant experiment results revealed that inoculation with phytohormone producing Bacillus spp. strains demonstrated substantial growth improvement of wheat biomass, number of spikes, and dry weight of shoots and roots. Results of this study indicate the biocontrol and biofertilizer potential of Bacillus spp. for sustainable plant nutrient management, growth promotion, and effective biocontrol of crop plants, particularly cultivated in the South Asian region.

Applications of endophytic microbes in agriculture, biotechnology, medicine, and beyond

Endophytes are emerging as integral components of plant microbiomes. Some of them play pivotal roles in plant development and plant responses to pathogens and abiotic stresses, whereas others produce useful and/or interesting secondary metabolites. The appreciation of their abilities to affect plant phenotypes and produce useful compounds via genetic and molecular interactions has paved the way for these abilities to be exploited for health and welfare of plants, humans and ecosystems. Here we comprehensively review current and potential applications of endophytes in the agricultural, pharmaceutical, and industrial sectors. In addition, we briefly discuss the research objectives that should be focused upon in the coming years in order for endophytes and their metabolites to be fully harnessed for potential use in diverse areas.

Plant growth-promoting bacterial endophytes as biocontrol agents of pre- and post-harvest diseases: Fundamentals, methods of application and future perspectives

Sustainable agriculture requires the recruitment of bacterial agents to control diverse plant diseases such as bacterial endophytes. Bacterial endophytes colonize and inhabit internal plant tissues without causing any apparent damage. Within the plant, these bacteria exert multiple beneficiary effects, including direct stimulation of plant growth by the action of phytohormones or the production of metabolites. However, bacterial endophytes also protect their plant host through biocontrol pathogens or by inducing plant innate immune system. The present work makes a systematic and in-depth review on the current state of endophytic bacterial diversity, their plant colonization strategies, and their potential roles as protective agents against plant diseases during pre- and post-harvest stages of crop productivity. In addition, an exploration of their beneficial effects on sustainable agriculture by reducing/eliminating the use of toxic agrochemicals was conducted. Finally, we propose diverse effective strategies for the application of endophytic bacteria as biological agents during both pre- and post-harvest stages, with the aim of protecting crop plants and their agricultural products.

The impact of the endophytic bacterial community on mulberry tree growth in the Three Gorges Reservoir ecosystem, China

Plant-associated microbes influence plant performance and may also impact biotic and abiotic stress tolerance. The microbiome of mulberry trees planted for ecological restoration in the hydro-fluctuation belt of the Three Gorges Reservoir Region, China, exhibited distinct patterns of localization. The endosphere exhibited lower α-diversity relative to the rhizosphere, but was more closely related to host growth status, especially in stem tissues. Pantoea was the predominant bacterial genus inhabiting the stems of two well-growing plants, while sequences identified as Pseudomonas and Pantoea were abundant in poorly growing plants. The complexity of the endophytic community was more connected to growth status in well-growing plants than it was in poorly growing plants. Among 151 endophytes cultured from collected samples of mulberry, 64 exhibited plant growth-promoting (PGP) potential in vitro and the majority of beneficial taxa were harvested from well-growing plants. Collectively, the present study indicates that the recruitment of beneficial endophytes may contribute to mulberry fitness under abiotic stress, and it provides a foundation for the development of a new strategy in vegetation restoration.

Antifungal Mechanism of Dipicolinic Acid and Its Efficacy for the Biocontrol of Pear Valsa Canker

Valsa pyri is a fatal canker pathogen that causes significant reduction of crop yield in pear orchards. V. pyri invades the trunk phloem, and is difficult to control by chemical treatment. In this work, it was found for the first time that Bacillus subtilis-produced dipicolinic acid (DPA) exhibits antifungal activity against different canker pathogens, including Alteraria alternata, Botryosphaeria dothidea, Rhizoctonia solani, and V. pyri. Growth inhibition of V. pyri was observed at less than 5 mM concentration (pH = 5.6). DPA showed the highest antifungal activity at acidic pH values and in the presence of bivalent metals, such as zinc(II), cobalt(II), and copper(II). Measurement of mRNA expression levels and scanning electron microscope (SEM) observations revealed that DPA causes V. pyri apoptosis via inhibition of chitin biosynthesis and subsequent cell lysis. Interestingly, DPA showed high stability in the pear bark and was able to cross the pear tree bark into the phloem, protecting the internal phases of the pear trunk. In preventive applications, DPA reduced the canker symptoms of V. pyri on Cuigan pear trees by 90%. Taken together, an efficient strategy for the management of V. pyri-caused canker disease was developed using a novel antifungal agent, DPA, with strong antifungal activity and particular diffusion properties.

Biocontrol Potential of a Novel Endophytic Bacterium From Mulberry (Morus) Tree

Mulberry (Morus) is an economically important woody tree that is suitable for use in sericulture as forage and in medicine. However, this broad-leaved tree is facing multiple threats ranging from phytopathogens to insect pests. Here, a Gram-positive, endospore-forming bacterium (ZJU1) was frequently isolated from healthy mulberry plants by screening for foliar endophytes showing antagonism against pathogens and pests. Whole-genome sequencing and annotation resulted in a genome size of 4.06 Mb and classified the bacterium as a novel strain of Bacillus amyloliquefaciens that has rarely been identified from tree leaves. An integrative approach combining traditional natural product chemistry, activity bioassays, and high-resolution mass spectrometry confirmed that strain ZJU1 uses a blend of antimicrobials including peptides and volatile organic compounds to oppose Botrytis cinerea, a major phytopathogenic fungus causing mulberry gray mold disease. We showed that the inoculation of endophyte-free plants with ZJU1 significantly decreased both leaf necrosis and mortality under field conditions. In addition to the direct interactions of endophytes with foliar pathogens, in planta studies suggested that the inoculation of endophytes also induced plant systemic defense, including high expression levels of mulberry disease resistance genes. Moreover, when applied to the generalist herbivore Spodoptera litura, ZJU1 was sufficient to reduce the pest survival rate below 50%. A previously undiscovered crystal toxin (Cry10Aa) could contribute to this insecticidal effect against notorious lepidopteran pests. These unique traits clearly demonstrate that B. amyloliquefaciens ZJU1 is promising for the development of successful strategies for biocontrol applications. The search for new plant-beneficial microbes and engineering microbiomes is therefore of great significance for sustainably improving plant performance.

Diversity of cultivable endophytic bacteria in mulberry and their potential for antimicrobial and plant growth-promoting activities

Endophytic bacteria-based biocontrol is regarded as a potential plant disease management strategy. Present study analyzed the diversity of mulberry endophytic bacteria basing on a culture-dependent approach and further evaluated their antimicrobial and plant growth-promoting (PGP) activities. A total of 608 cultivable endophytic bacteria, belonging to 4 phyla and 36 genera, were isolated from four mulberry cultivars having different resistance to sclerotiniosis in three seasons. Taxonomic compositional analysis results showed that Proteobacteria, Firmicutes, and Actinobacteria were the three dominant bacterial phyla in all communities, with the representative genera Pantoea, Bacillus, Pseudomonas, Curtobacterium, and Sphingomonas. Diversity analysis results indicated that the diversity of winter community was higher than that of spring or autumn, and higher diversities were detected in the resistant cultivar communities compared with the susceptible cultivar. Antagonism assays results showed that 33 isolates exhibited strong and stable activity against three phytopathogens which are Sclerotinia sclerotiorum, Botrytis cinerea, and Colletotrichum gloeosporioide. Eight endophytic bacteria were selected out from 33 antagonists based on the evaluation of antagonistic and PGP activities. Furthermore, pot experiment results revealed that all the 8 tested endophytes stimulated the growth of mulberry seedlings at different levels, and Bacillus sp. CW16-5 exhibited the highest promotion capacity, which the shoot length and the root fresh weight were increased by 83.37% and 217.70%, respectively. Altogether, present study revealed that mulberry harbors a large amount of diverse cultivable endophytic bacteria and they also serve as novel sources of beneficial bacteria and bioactive metabolites.

A Microbiome Study Reveals Seasonal Variation in Endophytic Bacteria Among different Mulberry Cultivars

Knowledge of seasonal shifts in the bacterial community composition among different mulberry (Morus L.) cultivars will facilitate to develop the biocontrol phytopathogens strategy using endophytic bacteria. The present study investigated the endophytic bacterial communities of four mulberry cultivars that have different resistance to mulberry fruit sclerotiniosis using Illumina-based sequencing of the 16S rRNA gene fragment in spring and autumn. The results indicated that spring samples harbor higher bacterial operational taxonomic units (OTUs), α-diversity, and bacterial community complexity in comparison with autumn samples. The taxonomic composition analysis showed that the majority of endophytes were composed of Proteobacteria (genus level: Methylobaterium) and Actinobacteria in spring, while sequences classified as Proteobacteria (genus level: Pantoea and Pseudomonas) were abundant in autumn. Analysis of β-diversity also revealed endophytic bacteria were divided into two main groups by season. By comparison among different mulberry cultivars, we found that Pantoea, Methylobaterium, and Pseudomonas were the three major bacterial genera in all cultivars, while their relative abundances varied with cultivars and appeared no obvious relationship with resistance level of mulberry fruit sclerotiniosis. The complex correlation of the endophytic communities in susceptible mulberry cultivars was higher than that of the resistant cultivars. Overall, the findings suggested that season plays a key role in determining the mulberry endophytic bacterial communities, followed by host cultivar, and Proteobacteria was the predominant phylum in both seasons and different mulberry cultivars.

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Season played a key role in determining mulberry endophytic bacterial communities.

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Mulberry endophytic bacterial variation was not obviously related with cultivars.

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Mulberry recruited beneficial endophytes as potential biocontrol agents.