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Nearly all plants and their organs are inhabited by endophytic microbes which play a crucial role in plant fitness and stress resilience. Harnessing endophytic services can provide effective solutions for a sustainable increase in agriculture productivity and can be used as a complement or alternative to agrochemicals. Shifting agriculture practices toward the use of nature-based solutions can contribute directly to the global challenges of food security and environmental sustainability. However, microbial inoculants have been used in agriculture for several decades with inconsistent efficacy. Key reasons of this inconsistent efficacy are linked to competition with indigenous soil microflora and inability to colonize plants. Endophytic microbes provide solutions to both of these issues which potentially make them better candidates for microbial inoculants. This article outlines the current advancements in endophytic research with special focus on endophytic bacilli. A better understanding of diverse mechanisms of disease control by bacilli is essential to achieve maximum biocontrol efficacy against multiple phytopathogens. Furthermore, we argue that integration of emerging technologies with strong theoretical frameworks have the potential to revolutionize biocontrol approaches based on endophytic microbes. [ABSTRACT FROM AUTHOR]

The beneficial interactions between plant and endophytes can enormously improve plant resistance against phytopathogens. Endophytic bacteria are well known for their plant propitious attributes. A tobacco seed endophyte Bacillus amyloliquefaciens YN201732 can enhance the ability of tobacco plants to resist powdery mildew, but the mechanisms operating at molecular level are highly elusive. In this study, transcriptome of YN201732-treated and non-treated tobacco leaves were compared under pathogen challenge and control conditions. Overall, analysis elucidates that DEGs related to biosynthesis of secondary metabolites, plant hormone signal transduction, phenylpropanoid biosynthesis, flavonoid biosynthesis, metabolic pathways, immune system process, and disease resistance-related biological functions were enriched in endophyte-treated diseased plant. The key genes of JA/ET pathway were significantly upregulated in tobacco plant after endophyte YN201732 treatment, which indicates the activation of JA/ET-mediated disease resistance against powdery mildew. Additionally, chitinase gene and synthesis of lignin and flavonoids were increased in diseased plant upon endophyte treatment which could help plant to resist pathogen infection. In conclusion, the study provides the molecular dissection of B. amyloliquefaciens YN201732-induced resistance in tobacco plant against powdery mildew and lays a theoretical foundation of employing endophytic bacteria against plant diseases. [ABSTRACT FROM AUTHOR]

Background: Native endophytes from maize could play a vital role in plant protection and growth promotion. The present study was undertaken to elucidate the effect of soil types and different maize varieties on culturable endophytic bacterial diversity and to use potential endophytes as biocontrol agents and plant growth promoters. Results: Based on rpoB and 16S rRNA genes, one hundred seventy-four (174) endophytes distributed into twenty-five (25) genera were identified, in which the greatest number of isolates were classified into Bacillus (52.30%), followed by Streptomyces (13.22%), Paenibacillus (6.32%), and Pseudomonas (4.60%). Out of the total isolated strains, endophytic strains with total number thirteen (13), eighty-four (84), one hundred and five (105), and nine (9) were able to fix nitrogen, and solubilize calcium phosphate, calcium phytate, and potassium, respectively. Moreover, out of total endophytes; twenty-four (24), thirty-three (33) and twenty-one (21) endophytic strains displayed marked antagonistic effects against important fungal pathogens such as Fusarium graminearum, Rhizoctonia solani and Exserohilum turcicum, respectively. Conclusions: Soil types play a functional role in culturable endophyte diversity and provide an isolation reference for endophytic reserves with multiple functions such as growth promoters and biocontrol agents. [ABSTRACT FROM AUTHOR]

Highlights: The endophytic community in apple leaves relates to geographic locations, apple varieties, and environment, providing the basis to explain the mechanisms underlying the establishment of apple endophytic communities and may help to devise apple disease management strategies. The dominant culturable endophytic bacteria Bacillus velezensis and B. subtilis successfully inhibit not only apple pathogens Alternaria alternata, Botryosphaeria dothidea, Valsa mali, Fusarium oxysporum, F. solani, and Rosellinia necatrix, but also F. oxysporum f. sp. cubense (banana Fusarium wilt) and Phytophthora nicotianae (tobacco black shank). The endophytic bacteria in apple leaves from apple-producing areas of Yunnan, China were isolated and identified on the basis of bacterial colony morphology and nucleotide sequences of 16S rRNA and rpoB genes. The endophytic bacterial isolates with nitrogen, phosphorus, and potassium utilization abilities were screened by culturing on functional media. A total of 5709 isolates of culturable endophytic bacteria (CEB) were isolated from 30 apple leaf samples collected from different regions. A total of 39 CEB representative isolates were identified as Bacillus velezensis, B. subtilis, B. licheniformis, B. safensis, B. pumilus, and Priestia megaterium. Among them, B. velezensis and B. subtilis were the main CEB, accounting for 55.00% and 34.37%, respectively, which exhibited potential inhibition on not only the main apple disease pathogens of Alternaria alternata, Valsa mali, Fusarium oxysporum, and Rosellinia necatrix, but also some important and uncontrollable phytopathogens, including F. oxysporum f. sp. cubense that causes banana Fusarium wilt, and Phytophthora nicotianae that causes tobacco black shank. Among these isolated endophytic bacteria species, a total of 10 strains, including b3, b4, b16, b17, b20, and b23 of B. subtilis, b7, b24, and b28 of B. licheniformis, and b38 of B. velezensis, can fix nitrogen; 8 strains, including b7 and b28 of B. licheniformis, b5, b10, and b23 of B. subtilis, b8 of B. safensis, and b6 of Priestia megaterium, could dissolve inorganic phosphorus; 11 strains, including b9, b12, b14, b30, b34, and b43 of B. velezensis, b6 of Priestia megaterium, and b17, b18, b20, and b26 of B. subtilis, could degrade organic phosphorus; and 5 strains, including b4, b5, and b26 of B. subtilis, and b7 and b28 of B. licheniformis could dissolve potassium. These strains are valuable resources of endophytic bacteria that have adapted to the ecological environment of the Cold Plateau apple-production area and could be used as plant disease biocontrol agents and biofertilizers of crops. The culturable phyllosphere endophytes in apple leaves relate to geographic locations, apple varieties, and environment, providing the basis to explain the mechanisms underlying the establishment of apple endophyte diversity and may help to devise apple disease management strategies. [ABSTRACT FROM AUTHOR]

Bacterial leaf streak (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc), impacts the production of rice. However, several rice cultivars displayed resistance to Xoc in the field, but scarce information is available about the role of endophytic microbiota in disease resistance. In the present study, the endophytic bacterial communities of resistant and susceptible rice cultivars "CG2" and "IR24", respectively, were analyzed using high throughput 16S rRNA gene amplified sequencing and culture dependent method was further used for bacterial isolation. A total of 452,716 high-quality sequences representing 132 distinct OTUs (Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes) and 46 isolates of 16 genera were explored from rice leaves infected with Xoc. Community diversity of endophytic bacteria were higher in the leaves of the resistant cultivars compared to susceptible cultivars upon Xoc infection. Strikingly, this diversity might contribute to natural defense of the resistant cultivar against pathogen. Pantoea, which is pathogen antagonist, was frequently detected in two cultivars and higher abundance were recorded in resistant cultivars. Different abundance genus includes endophytic isolates with marked antagonistic activity to Xoc. The increased proportions of antagonistic bacteria, may contribute to resistance of rice cultivar against Xoc and the Pantoea genus was recruited by Xoc infection play a key role in suppressing the development of BLS disease in rice. Taken together, this work reveals the association between endophytic bacteria and BLS resistance in rice and identification of antagonism-Xoc bacterial communities in rice. [ABSTRACT FROM AUTHOR]

Bacillus amyloliquefaciens YN201732 is an endophytic bacteria with high biocontrol efficiency and broad-spectrum antimicrobial activities. In order to clarify the main active ingredients and their antifungal mechanisms against powdery mildew of tobacco, this study is focused on lipopeptide obtained through acid precipitation and organic solvent extraction. HPLC and LCMS-IT-TOF were used to separate and identify antimicrobial lipopeptides. Findings revealed that bacillomycin D plays an important role against surrogate fungal pathogen Fusarium solani. Synthetic pathways of sfp, bacillomycin D, and fengycin were separately disrupted. The sfp gene knockout mutant B. amyloliquefaciens YN201732M1 only showed minor antagonistic activity against F. solani. While Erysiphe cichoracearum spore germination was inhibited and pot experiments displayed a significant decrease in tobacco powdery mildew. The spore inhibition rate of YN201732M1 was only 30.29%, and the pot experiment control effect was less than 37.39%, which was significantly lower than that of the wild type. The inhibitory effect of mutant YN201732M2 (deficient in the production of bacillomycin D) and mutant YN201732M3 (deficient in the production of fengycin) on the spore germination of E. cichoracearum were 50.22% and 53.06%, respectively, suggesting that both fengycin and bacillomycin D had potential effects on spore germination of powdery mildew. Interestingly, in a greenhouse assay, both B. amyloliquefaciens YN201732M2 and YN201732M3 mutants displayed less of a control effect on tobacco powdery mildew than wild type. The results from in vitro , spore germination, and greenhouse-pot studies demonstrated that antimicrobial lipopeptides especially bacillomycin D and fengycin may contribute to the prevention and control of tobacco powdery mildew. In addition, gene mutation related to lipopeptide synthesis can also affect the biofilm formation of strains. [ABSTRACT FROM AUTHOR]

Huanglongbing (HLB) is one of the most serious diseases affecting citrus trees worldwide. The causal agent of HLB is the nonculturable endophytic bacterium Candidatus Liberibacter asiaticus (C las) and Diaphorina citri (Asian citrus psyllid, ACP) its insect vector. In this study, we investigated the seasonal variations in the population dynamics of C las and assessed the possible genetic variations among the identified isolates. We conducted a disease survey in tangerine citrus groves affected with HLB in Binchuan county, Yunnan province, China, on a monthly basis over a period of one year. The collected leaf samples were analyzed every month via nested PCR, targeting the 16S rRNA and the β-operon ribosomal protein-encoding genes of C las. The abundance of the HLB-causing pathogen changes several times, with high temperature in July 2017 yielding low pathogen abundance, followed by a high peak in December and January 2017-18. The number of bacteria inside each tree was inconsistent, showing drastic variations every month. C las-negatively affected the endophytic microbial communities inside the citrus trees. There could be a direct relationship between the low number of endophytes and the high number of pathogens present inside each tree. Moreover, the genetic diversity of C las can be used to elucidate the pattern and epidemiology of this pathogen in different regions. The obtained sequences were phylogenetically related to other sequences from China. A comparison of C las gene sequences revealed little variation among the isolates circulating in China. The primers used in this study did not show cross-reactivity with other plant pathogens or with endophytes isolated from citrus trees. In addition, no mismatches were observed when an in silico analysis was performed. In summary, this is the first report of the seasonal variation of HLB-causing pathogen in tangerine citrus varieties in China. Environmental influences and endophyte acquisition during different months help us understand the C las population during different seasons, and to improve pathogen detection. The monthly fluctuations in pathogen abundance could aid in the design of proper management strategies in the field. • Candidatus Liberibacter asiaticus is fastidious and phloem-limited pathogen causing huanglongbing. • The monthly fluctuations of pathogen in tangerine varieties affected with this disease was investigated. • Genetic diversity of pathogen circulating in the study area was also revealed. • HLB negatively affected the indigenous endophytes population. • The monthly fluctuations in pathogen could aid in the design of management strategies. [ABSTRACT FROM AUTHOR]

Huanglongbing (HLB) pathogen Candidatus Liberibacter asiaticus (CLas) brings a great concern about the phloem nutrient transport in diseased plants. There is an urgent need to find the best management strategies to reduce the losses in the citrus industry worldwide. Endophytic bacteria are negatively affected by CLas pathogen, and these endophytes are associated with improved availability of nutrients and pathogen resistance. This study underpins the relationship between CLas pathogen, endophyte population and nutrients availability in citrus plants. The citrus plants were treated with Bacillus subtilis L1-21 and Hoagland solution to find out synergism efficacy to mitigate citrus HLB. We showed that citrus shoots in the presence of 50% Hoagland solution displayed maximum number of endophytes with 6.28 × 103 to 3.04 × 105 CFU/g. Among 50 candidate strains, B. subtilis L1-21 emerged as potential antagonist against surrogate strain Xanthomonas citri subsp. citri. The citrus half-leaf method identified that application of endophyte L1-21 with 50% Hoagland solution successfully reduces the CLas abundance. We point out that this combination results in a higher number of endophytes population with 2.52 × 104 to 9.11 × 106 CFU/g after 60 days, and reduces CLas pathogen abundance in asymptomatic HLB plants. In HLB symptomatic citrus plants, B. subtilis L1-21 potentially increases the endophyte population from 1.11 × 104 to 5.26 × 107 CFU/g in the presence of Hoagland solution, and pathogen abundance was reduced from 9.51 × 105 to 1.06 × 104 copies/g. Altogether, we suggested that the presence of endophyte L1-21 with Hoagland solution is more effective in HLB asymptomatic citrus plants, but a slight reduction of pathogen was observed in symptomatic plants. The findings revealed the role of indigenous citrus endophyte B. subtilis L1-21 along with other nutrients in the reduction of CLas pathogen abundance inside symptomatic and asymptomatic plants in citrus endophyte–nutrient–pathogen interplay. [ABSTRACT FROM AUTHOR]

• Metabolomics approaches were employed to gain insight into mechanisms involved in citrus defense. • Potential changes in diseased plants were observed with Bacillus subtilis L1-21. • Metabolites up-regulated were xanthine, leucic acid, and α-Linolenic acid • Changes in diseased citrus physiology after endophyte L1-21 could give us future direction. Huanglongbing (HLB) is one of the most serious citrus diseases, caused by phloem limited endophytic bacteria Candidatus Liberibacter asiaticus (C las), affecting worldwide citrus production. Metabolomics approaches were employed to gain insight into mechanisms involved in defense against C las in endophyte Bacillus subtilis L1-21 treated diseased and healthy citrus plants. Using LC-ESI-MS/MS, we compared the metabolic profile of citrus plants before and after treatment with endophyte L1-21. Our analysis indicated large differences in citrus metabolites after endophyte L1-21 application. In total, seven hundred and fourty two metabolites were detected with highest percentage recorded for organic acids, flavone, amino acid derivatives, flavone C-glycosides, nucleotide derivatives, and flavonol. Interestingly, differentially expressed metabolites (DEMs) analysis revealed the amino acids, such as lysine and tyrosine which are involved in plant defense agianst pathogen attack were regulated in diseased citrus plants after endophyte application (padj<0.05). In addition, other important metabolites up-regulated were xanthine, leucic acid, and α-Linolenic acid implicated in different plant defense pathways against C las. Furhter, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed important pathways related to purine metabolism, biotin metabolism, and betalain biosynthesis, terpenoid-quinone biosynthesis, phenylalanine, tyrosine and lysine biosynthesis, isoflavonoid biosynthesis (padj<0.05). Taken together, this is the first study using native endophytes in diseased and healthy state of citrus which has proven to be useful in disease management by strengthening the defense of citrus to C las pathogen. [ABSTRACT FROM AUTHOR]

• Bacillus amyloliquefaciens YN201732, a beneficial endophyte isolated from tobacco seeds can control tobacco powdery mildew. • This endophyte can also promote seed germination and seedling plant growth. • Important genes were induced involved in jasmonic acid/ethylene signaling pathway of plant. • Polyphenol oxidase and chitinases are closely related to tobacco induced resistance to powdery mildew. • B. amyloliquefaciens YN201732 has high potential to be used as biocontrol agent in tobacco agriculture. The effectiveness of Bacillus amyloliquefaciens YN201732, a beneficial endophyte isolated from tobacco seeds was explored for control of tobacco powdery mildew and the systemic resistance mechanisms involved. The results of the study showed that endophyte YN201732 has antagonistic effects on 12 pathogenic fungi. The fermentation broth can inhibit the spore germination and has good control effect on tobacco powdery mildew in the greenhouse. The control effect of the protective test and the therapeutic test at 14 days reached up to 71.09% and 86.11%, respectively. Moreover, endophyte YN201732 can also promote seed germination and seedling plant growth, and improve plant photosynthesis. Compare with water treatment, the root length, plant height, maximum leaf length, leaf width, fresh weight, dry weight, chlorophyll and net photosynthetic rate of tobacco seedlings increased by 32.27%, 86.67%, 154.92%, 107.25%, 664.71%, 207.69%, 150.33%, and 240%, respectively. Additionally, the expression of NPR1 in tobacco leaves was stable when inoculated with YN201732 at different time points, while the PDF1.2 gene was up-regulated rapidly, suggesting that jasmonic acid/ethylene signaling pathway of plant might be induced, which enhance plant resistance to powdery mildew. The chit and PPO genes were highly expressed while the PAL and POD defense enzyme genes were down-regulated, the expression of chit was up-regulated 30–70 times after induction treatment. In addition, we revealed that polyphenol oxidase and chitinases are closely related to tobacco induced resistance to powdery mildew. Thus, our study showed that B. amyloliquefaciens YN201732 has high potential to be used as biocontrol agent and plant-growth promoting bacterium in tobacco agriculture. [ABSTRACT FROM AUTHOR]