Isolation and Identification of Endophytic Bacteria with Plant Growth Promoting Activity and Biocontrol Potential from Wild Pistachio Trees

Evaluating Plant Growth-Promoting Rhizobacteria to Improve the Productivity of Forage Pearl Millet

India's livestock industry is grappling with a shortage of green fodder, necessitating concerted efforts to boost organized production and ensure a sufficient supply of high-quality forages, crucial for formulating nutritionally balanced, cost-effective, and rumen-healthy animal diets. Hence, this study was conducted to assess the plant growth-promoting characteristics of liquid microbial inoculants and their impact on the yield of forage pearl millet. The bacterial cultures utilized included Sphingobacterium sp., Stenotrophomonas maltophilia, and an isolate from vegetable cowpea, subsequently identified as Burkholderia seminalis. These cultures were initially characterized for their plant growth-promoting traits at different temperature and physiological conditions. All the bacterial cultures were found promising for PGPR traits over varied temperature conditions and the optimum activity was recorded at 40 °C, with tolerance to saline and drought stresses as well as wide pH and temperature ranges. A field experiment was conducted during kharif 2020 at Punjab Agricultural University, Ludhiana and Punjab Agricultural University, Regional Research Station, Bathinda, involving combinations of liquid microbial inoculants along with 100% Recommended Dose of Fertilizer (RDF). It was observed that the treatment including B. seminalis + S. maltophilia along with RDF yielded the highest green fodder and dry matter yield, In conclusion, it is evident that the utilization of these liquid microbial inoculants holds significant potential for playing a pivotal role in the integrated nutrient management of forage pearl millet, thereby contributing to heightened productivity and sustained soil health.

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.

Pathogen Eradication in Garlic in the Phytobiome Context: Should We Aim for Complete Cleaning?

Global food production is challenged by plant pathogens that cause significant crop losses. Fungi, bacteria, and viruses have long threatened sustainable and profitable agriculture. The danger is even higher in vegetatively propagated horticultural crops, such as garlic. Currently, quarantine, rouging infected plants, and control of natural vectors are used as the main means of disease and pest control in garlic crops. Agricultural biotechnology, meristem-tip culture, and cryotherapy offer solutions for virus eradication and for the multiplication of 'clean stocks', but at the same time, impact the symbiotic and beneficial components of the garlic microbiome. Our research involves the first metatranscriptomic analysis of the microbiome of garlic bulb tissue, PCR analyses, and a biological assay of endophytes and pathogens. We have demonstrated that in vitro sanitation methods, such as shoot tip culture or cryotherapy can alter the garlic microbiome. Shoot tip culture proved ineffective in virus elimination, but reduced bacterial load and eliminated fungal infections. Conversely, cryotherapy was efficient in virus eradication but demolished other components of the garlic microbiome. Garlic plants sanitized by cryotherapy exhibited a lower survival rate, and a longer in vitro regeneration period. The question arises whether total eradication of viruses, at the expense of other microflora, is necessary, or if a partial reduction in the pathogenic load would suffice for sanitized garlic production. We explore this question from both scientific and commercial perspectives.

Effectiveness of Phosphate and Zinc Solubilizing Paenarthrobacter nitroguajacolicus P1 as Halotolerant Rhizobacterium with Growth-Promoting Activity on Pistacia vera L

Plant growth-promoting rhizobacteria (PGPR) are beneficial microorganisms to develop microbial fertilizers. Biofertilizers can accelerate plant growth and enhance crop yields. The current research aimed to isolate and identify rhizobacterium with plant growth-promoting activity in the rhizospheric region of pistachio trees in arid and salty region of Iran. In the present study, 26 bacterial isolates were isolated from the rhizospheric region of the pistachio trees. Plant growth-promoting characteristics of isolated bacteria, including the ability to solubilize phosphate and zinc, produce hydrolyzing enzymes, and hydrogen cyanide (HCN), as well as synthesize indole-3-acetic acid (IAA) were evaluated through in vitro assays. Based on these activities, five multifunctional bacterial strains designated P1, P10, P11, P17, and P19 were then applied and their effect was studied on the growth and physiological properties of Pistacia vera L. seedlings by pot experiments under normal conditions. Finally, the most efficient strain has been identified by analysis of the 16S rRNA gene sequence. According to the results, all the isolated bacteria exhibited considerable plant growth-promoting properties. They could produce amylase (n = 26, 2 ± 0.00-13 ± 0.42 mm), lipase (n = 24, 2 ± 0.00-9 ± 0.23 mm), protease (n = 20, 1 ± 0.00-17 ± 0.0 mm), indole-3-acetic acid (n = 26, ranging from 5.05 ± 0.08 to 11.5 ± 0.11 μg/mL) and HCN (n = 24). Six isolates showed significant growth at 20% w/v NaCl. Inoculation of P1, P17, and P19 increased chlorophyll, carotenoid, and phenolic content in treated Pistacia vera L. seedlings. P1 and P11 inoculated plants showed an enhanced level of anthocyanin and proline. These most effective strains were catalase and Gram-positive bacterium and showed antibiotic sensitivity. They can consider as halotolerant PGPR, due to the growth in the presence of NaCl (20% w/v). Finally, P1 inoculated plants exhibited higher levels of sugar content. This strain showed the most similarity (99.92%-1322 bp) to Paenarthrobacter nitroguajacolicus based on 16S rRNA gene sequence. Based on the results, Paenarthrobacter nitroguajacolicus P1 with multiple PGPR can be applied as a promising candidate in the soil-Pistacia vera L. system to improve their productivity and health by increasing available nutrient content, improving photosynthetic parameters, and producing phytohormones and HCN.

Stenotrophomonas in diversified cropping systems: friend or foe?

In the current scenario, the use of synthetic fertilizers is at its peak, which is an expensive affair, possesses harmful effects to the environment, negatively affecting soil fertility and beneficial soil microfauna as well as human health. Because of this, the demand for natural, chemical-free, and organic foods is increasing day by day. Therefore, in the present circumstances use of biofertilizers for plant growth-promotion and microbe-based biopesticides against biotic stresses are alternative options to reduce the risk of both synthetic fertilizers and pesticides. The plant growth promoting rhizobacteria (PGPR) and microbial biocontrol agents are ecologically safe and effective. Owning their beneficial properties on plant systems without harming the ecosystem, they are catching the widespread interest of researchers, agriculturists, and industrialists. In this context, the genus Stenotrophomonas is an emerging potential source of both biofertilizer and biopesticide. This genus is particularly known for producing osmoprotective substances which play a key role in cellular functions, i.e., DNA replication, DNA-protein interactions, and cellular metabolism to regulate the osmotic balance, and also acts as effective stabilizers of enzymes. Moreover, few species of this genus are disease causing agents in humans that is why; it has become an emerging field of research in the present scenario. In the past, many studies were conducted on exploring the different applications of Stenotrophomonas in various fields, however, further researches are required to explore the various functions of Stenotrophomonas in plant growth promotion and management of pests and diseases under diverse growth conditions and to demonstrate its interaction with plant and soil systems. The present review discusses various plant growth and biocontrol attributes of the genus Stenotrophomonas in various food crops along with knowledge gaps. Additionally, the potential risks and challenges associated with the use of Stenotrophomonas in agriculture systems have also been discussed along with a call for further research in this area.

Diversity and Biocontrol Potential of Endophytic Fungi and Bacteria Associated with Healthy Welsh Onion Leaves in Taiwan

Foliar diseases caused by Stemphylium and Colletotrichum species are among the major biotic factors limiting Welsh onion production in Taiwan. Owing to concerns about the environment and the development of pathogen resistance to existing fungicides, biological control using endophytes is emerging as an eco-friendly alternative to chemical control. The aim of the present study was to isolate endophytes from healthy Welsh onion leaves and investigate their antagonistic potential against the major phytopathogenic fungi associated with Welsh onion plants in Taiwan. A total of 109 bacterial and 31 fungal strains were isolated from healthy Welsh onion leaves and assigned to 16 bacterial and nine fungal genera using morphological and molecular characterization based on DNA sequence data obtained from nuclear internal transcribed spacer (nrITS) (fungi) and 16S rRNA (bacteria). Evaluation of these endophytic isolates for biocontrol activity against leaf blight pathogens Colletotrichum spaethianum strain SX15-2 and Stemphylium vesicarium strain SX20-2 by dual culture assay and greenhouse experiments resulted in the identification of two bacterial isolates (GFB08 and LFB28) and two fungal isolates (GFF06 and GFF08) as promising antagonists to leaf blight pathogens. Among the four selected isolates, Bacillus strain GFB08 exhibited the highest disease control in the greenhouse study. Therefore, Bacillus strain GFB08 was further evaluated to understand the mechanism underlying its biocontrol efficacy. A phylogenetic analysis based on six genes identified Bacillus strain GFB08 as B. velezensis. The presence of antimicrobial peptide genes (baer, bamC, bmyB, dfnA, fenD, ituC, mlna, and srfAA) and the secretion of several cell wall degrading enzymes (CWDEs), including cellulase and protease, confirmed the antifungal nature of B. velezensis strain GFB08. Leaf blight disease suppression by preventive and curative assays indicated that B. velezensis strain GFB08 has preventive efficacy on C. spaethianum strain SX15-2 and both preventive and curative efficacy on S. vesicarium strain SX20-2. Overall, the current study revealed that healthy Welsh onion leaves harbour diverse bacterial and fungal endophytes, among which the endophytic bacterial strain, B. velezensis strain GFB08, could potentially be used as a biocontrol agent to manage the leaf blight diseases of Welsh onion in Taiwan.

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.

Fungicide sensitivity of grapevine bacteria with plant growth-promoting traits and antagonistic activity as non-target microorganisms

This study evaluates the capacity of commercial formulations of synthetic fungicides to inhibit grapevine bacterial growth when sprayed on vineyards to control diseases, such as downy mildew, powdery mildew and secondary rots. Fungicide sensitivity plate assays were carried out on bacteria isolated from vineyards that were also identified and characterized for their plant growth-promoting (PGP) traits and antifungal activity. The high taxonomic variability of bacteria screened with different chemical classes of fungicides is one new finding of this study. Seven out of 11 fungicides were able to inhibit the growth of bacteria at a concentration corresponding to the maximum dose allowed by law in spray treatments of vineyards. Bacterial sensitivity to each fungicide varied greatly. Many sensitive isolates displayed PGP traits and/or antagonistic activity. This study shows the potential impact of fungicidal treatments on grapevine bacterial microbiota. The involvement of bacteria beneficial to the growth and health of plants underlines the importance of this investigation. Our data reveal that the control of a certain disease may be possible using fungicides that have no or low impact on natural non-target microbiota. Understanding the action mechanisms of the active ingredients in these products is a priority for the development of new eco-friendly pesticides.

Biocontrol Potential of Bacillus subtilis and Bacillus tequilensis against Four Fusarium Species

The use of biological control agents as opposed to synthetic agrochemicals to control plant pathogens has gained momentum, considering their numerous advantages. The aim of this study is to investigate the biocontrol potential of plant bacterial isolates against Fusarium oxysporum, Fusarium proliferatum, Fusarium culmorum, and Fusarium verticillioides. Isolation, identification, characterization, and in vitro biocontrol antagonistic assays of these isolates against Fusarium species were carried out following standard protocols. The bacterial endophytes were isolated from Glycine max. L leaves (B1), Brassica napus. L seeds (B2), Vigna unguiculata seeds (B3), and Glycine max. L seeds (B4). The bacterial isolates were identified using 16S rRNA PCR sequencing. A phylogenetic analysis shows that the bacterial isolates are closely related to Bacillus subtilis (B1) and Bacillus tequilensis (B2-B4), with an identity score above 98%. All the bacterial isolates produced a significant amount (p < 0.05) of indole acetic acid (IAA), siderophores, and protease activity. In vitro antagonistic assays of these isolates show a significant (p < 0.05) growth inhibition of the fungal mycelia in the following order: F. proliferatum > F. culmorum > F. verticillioides > F. oxysporum, compared to the control. The results suggest that these bacterial isolates are good biocontrol candidates against the selected Fusarium species.

Genetic Determinants of Antagonistic Interactions and the Response of New Endophytic Strain Serratia quinivorans KP32 to Fungal Phytopathogens

Fungal phytopathogens are challenging to control due to their penetration into plant tissues. Therefore, plant-colonizing bacteria could serve as an excellent weapon in fighting fungal infections. In this study, we aim to determine the biocontrol potential of the new endophytic strain Serratia quinivorans KP32, isolated from the roots of Petroselinum crispum L.; identify the related mechanisms; and understand the basis of its antagonistic interaction with taxonomically diverse fungi at the molecular level. The KP32 strain presented biological activity against Rhizoctonia solani, Colletotrichum dematium, Fusarium avenaceum, and Sclerotinia sclerotiorum, and its ability to inhibit the growth of the phytopathogens was found to be mediated by a broad spectrum of biocontrol features, such as the production of a number of lytic enzymes (amylases, chitinases, and proteases), siderophores, volatile organic and inorganic compounds, salicylic acid, and N-acyl-homoserine lactones. The higher expression of chitinase (chiA) and genes involved in the biosynthesis of hydrogen cyanide (hcnC), enterobactin (entB), and acetoin (budA) in bacteria exposed to fungal filtrates confirmed that these factors could act in combination, leading to a synergistic inhibitory effect of the strain against phytopathogens. We also confirm the active movement, self-aggregation, exopolysaccharide production, and biofilm formation abilities of the KP32 strain, which are essential for effective plant colonization. Its biological activity and colonization potential indicate that KP32 holds tremendous potential for use as an active biopesticide and plant growth promoter.

Deciphering the potential of a plant growth promoting endophyte Rhizobium sp. WYJ-E13, and functional annotation of the genes involved in the metabolic pathway

Plant growth-promoting rhizobacteria (PGPR) are well-acknowledged root endophytic bacteria used for plant growth promotion. However, which metabolites produced by PGPR could promote plant growth remains unclear. Additionally, which genes are responsible for plant growth-promoting traits is also not elucidated. Thus, as comprehensive understanding of the mechanism of endophyte in growth promotion is limited, this study aimed to determine the metabolites and genes involved in plant growth-promotion. We isolated an endophytic Rhizobium sp. WYJ-E13 strain from the roots of Curcuma wenyujin Y.H. Chen et C. Ling, a perennial herb and medicinal plant. The tissue culture experiment showed its plant growth-promoting ability. The bacterium colonization in the root was confirmed by scanning electron microscopy and paraffin sectioning. Furthermore, it was noted that the WYJ-E13 strain produced cytokinin, anthranilic acid, and L-phenylalanine by metabolome analysis. Whole-genome analysis of the strain showed that it consists of a circular chromosome of 4,350,227 bp with an overall GC content of 60.34%, of a 2,149,667 bp plasmid1 with 59.86% GC, and of a 406,180 bp plasmid2 with 58.05% GC. Genome annotation identified 4,349 putative protein-coding genes, 51 tRNAs, and 9 rRNAs. The CDSs number allocated to the Kyoto Encyclopedia of Genes and Genomes, Gene Ontology, and Clusters of Orthologous Genes databases were 2027, 3,175 and 3,849, respectively. Comparative genome analysis displayed that Rhizobium sp. WYJ-E13 possesses the collinear region among three species: Rhizobium acidisoli FH23, Rhizobium gallicum R602 and Rhizobium phaseoli R650. We recognized a total set of genes that are possibly related to plant growth promotion, including genes involved in nitrogen metabolism (nifU, gltA, gltB, gltD, glnA, glnD), hormone production (trp ABCDEFS), sulfur metabolism (cysD, cysE, cysK, cysN), phosphate metabolism (pstA, pstC, phoB, phoH, phoU), and root colonization. Collectively, these findings revealed the roles of WYJ-E13 strain in plant growth-promotion. To the best of our knowledge, this was the first study using whole-genome sequencing for Rhizobium sp. WYJ-E13 associated with C. wenyujin. WYJ-E13 strain has a high potential to be used as Curcuma biofertilizer for sustainable agriculture.

Isolation and identification of a new biocontrol bacteria against Salvia miltiorrhiza root rot and optimization of culture conditions for antifungal substance production using response surface methodology

Background

S. miltiorrhiza root rot is a soil-borne disease mainly caused by Fusarium solani and Fusarium oxysporum, which has spread rapidly in China in recent years. To reduce the amount of pesticides to control this plant fungal disease, biological control using endophytic bacteria is a promising method. Many endophytic bacteria show good biocontrol potential against various plant fungal diseases. The aims of this study were to isolate and identify endophytic bacteria with antifungal activity from Salvia miltiorrhiza plant tissue. In order to increase antifungal substances production, the culture conditions of the isolated DS-R5 strain were optimized through response surface methodology.

Results

Thirteen endophytic bacteria with antifungal activity against the target pathogenic fungus were successfully screened. The DS-R5 strain that had the strongest antifungal activity was identified based on morphological, physiological and biochemical characteristics, 16S rRNA and gyrB sequence analysis.The results of response surface methodology experiments showed that the optimal values of the three significant factors were as follows: medium volume, 51.0 ml; initial pH, 6.7; fermentation temperature, 33.1 °C. Under these optimal culture conditions, the titer of antifungal substances produced by the DS-R5 strain was 77.6% higher than that under the initial culture conditions.

Conclusions

The antifungal activity of endophytic bacteria from Salvia miltiorrhiza has been demonstrated for the first time, which may benefit future crop quality and production. In addition, response surface methodology can be well applied the optimization of culture conditions for antifungal substance, which lays the foundation for further research on strain DS-R5.

Fungal disease suppression and growth promotion potential of endophytic bacteria from ethnomedicinal plants

103 bacterial isolates obtained from 8 ethnomedicinal plants in Manipur, India were studied for antifungal and plant growth promoting (PGP) activities. Forty-six (46), out of 62 antifungal isolates, showed potent activities against R. solani. Since R. solani (RS), a sheath blight pathogen, threatens rice yields worldwide, the present study was aimed at discovering promising bioinoculants with anti-RS and PGP potential on rice. Twenty-nine (29) endophytic isolates exhibiting promising anti-RS and PGP activities were subjected to seed vigor assays on rice (var. Jatra) and 16 were found to enhance rice seedling vigour by 70% or more over the control. Four (4) strains, Streptomyces sp. (AcRz21), Alkalihalobacillus sp. (PtL11), Bacillus sp. (TgIb5), and Priestia sp. (TgIb12) with the highest vigor indices were studied for growth promotion of rice in field conditions under pathogen-challenged and pathogen-free conditions. These bioactive strains were able to significantly enhance root and shoot biomass and reduce lesion heights caused by R. solani.

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.

Dynamics, phylogeny and phyto-stimulating potential of chitinase synthesizing bacterial root endosymbiosiome of North Western Himalayan Brassica rapa L

The less phytopathogen susceptibility in Himalayan Brassica rapa L. has made it an exceptional crop eluding synthetic pesticide inputs, thereby guarantying economically well-founded and ecologically sustainable agriculture. The relevance of niche microflora of this crop has not been deliberated in this context, as endosymbiosiome is more stable than their rhizosphere counterparts on account of their restricted acquaintance with altering environment; therefore, the present investigation was carried out to study the endophytic microfloral dynamics across the B. rapa germplasm in context to their ability to produce chitinase and to characterize the screened microflora for functional and biochemical comportments in relevance to plant growth stimulation. A total of 200 colonies of bacterial endophytes were isolated from the roots of B. rapa across the J&K UT, comprising 66 locations. After morphological, ARDRA, and sequence analysis, eighty-one isolates were selected for the study, among the isolated microflora Pseudomonas sp. Bacillus sp. dominated. Likewise, class γ-proteobacteria dominated, followed by Firmicutes. The diversity studies have exposed changing fallouts on all the critical diversity indices, and while screening the isolated microflora for chitinase production, twenty-two strains pertaining to different genera produced chitinase. After carbon source supplementation to the chitinase production media, the average chitinase activity was significantly highest in glycerol supplementation. These 22 strains were further studied, and upon screening them for their fungistatic behavior against six fungal species, wide diversity was observed in this context. The antibiotic sensitivity pattern of the isolated strains against chloramphenicol, rifampicin, amikacin, erythromycin, and polymyxin-B showed that the strains were primarily sensitive to chloramphenicol and erythromycin. Among all the strains, only eleven produced indole acetic acid, ten were able to solubilize tricalcium phosphate and eight produced siderophores. The hydrocyanic acid and ammonia production was observed in seven strains each. Thus, the present investigation revealed that these strains could be used as potential plant growth promoters in sustainable agriculture systems besides putative biocontrol agents.

Decoding the Plant Growth Promotion and Antagonistic Potential of Bacterial Endophytes From Ocimum sanctum Linn. Against Root Rot Pathogen Fusarium oxysporum in Pisum sativum

The present study demonstrates plant growth promotion and induction of systemic resistance in pea (Pisum sativum) plant against Fusarium oxysporum f.sp. pisi by two bacterial endophytes, Pseudomonas aeruginosa OS_12 and Aneurinibacillus aneurinilyticus OS_25 isolated from leaves of Ocimum sanctum Linn. The endophytes were evaluated for their antagonistic potential against three phytopathogens Rhizoctonia solani, F. oxysporum f. sp. pisi, and Pythium aphanidermatum by dual culture assay. Maximum inhibition of F. oxysporum f. sp. pisi was observed by strains OS_12 and OS_25 among all root rot pathogens. Scanning electron microscopy of dual culture indicated hyphal distortion and destruction in the case of F. oxysporum f. sp. pisi. Further, volatile organic compounds (VOCs) were identified by gas chromatography-mass spectrometry (GC-MS). The GC-MS detected eight bioactive compounds from hexane extracts for instance, Dodecanoic acid, Tetra decanoic acid, L-ascorbic acid, Trans-13-Octadecanoic acid, Octadecanoic acid. Both the endophytes exhibited multifarious plant growth promoting traits such as indole acetic production (30-33 μg IAA ml^-1), phosphate solubilization, and siderophore and ammonia production. Pot trials were conducted to assess the efficacy of endophytes in field conditions. A significant reduction in disease mortality rate and enhancement of growth parameters was observed in pea plants treated with consortium of endophytes OS_12 and OS_25 challenged with F. oxysporum f.sp. pisi infection. The endophytic strains elicited induced systemic resistance (ISR) in pathogen challenged pea plants by enhancing activities of Phenylalanine ammonia lyase (PAL), peroxidase (PO), polyphenol oxidase (PPO), ascorbate oxidase (AO), catalase (CAT) and total phenolic content. The endophytes reduced the oxidative stress as revealed by decrease in malondialdehyde (MDA) content and subsequently, lipid peroxidation in host plant leaves. Robust root colonization of pea seedlings by endophytes was observed by scanning electron microscopy (SEM) and fluorescence microscopy. Thus, plant growth promoting endophytic P. aeruginosa and A. aneurinilyticus can be further exploited through bio-formulations for sustainable protection of crops against root rot diseases as bio-control agents.

Culturable Bacterial Endophytes Associated With Shrubs Growing Along the Draw-Down Zone of Lake Bogoria, Kenya: Assessment of Antifungal Potential Against Fusarium solani and Induction of Bean Root Rot Protection

Vascular shrubs growing along the draw-down zones of saline lakes must develop adaptive mechanisms to cope with high salinity, erratic environmental conditions, and other biotic and abiotic stresses. Microbial endophytes from plants growing in these unique environments harbor diverse metabolic and genetic profiles that play an important role in plant growth, health, and survival under stressful conditions. A variety of bacterial endophytes have been isolated from salt tolerant plants but their potential applications in agriculture have not been fully explored. To further address this gap, the present study sought to isolate culturable bacterial endophytes from shrubs growing along the draw-down zone of Lake Bogoria, a saline alkaline lake, and examined their functional characteristics and potential in the biocontrol of the bean root rot pathogen, Fusarium solani. We collected shrubs growing within 5 m distance from the shoreline of Lake Bogoria and isolated 69 bacterial endophytes. The endophytic bacteria were affiliated to three different phyla (Firmicutes, Proteobacteria, and Actinobacteria) with a bias in the genera, Bacillus, and they showed no tissue or plant specificity. All selected isolates were positive for catalase enzyme grown in 1.5 M NaCl; three isolates (B23, B19, and B53) produced indole acetic acid (IAA) and only one isolate, B23 did not solubilize phosphate on Pikovskaya agar. Isolates, B19 and B53 exhibited more than 50% of mycelial inhibition in the dual culture assay and completely inhibited the germination of F. solani spores in co-culture assays while two isolates, B07 and B39 had delayed fungal spore germination after an overnight incubation. All isolates were able to establish endophytic association in the roots, stems, and leaves of been seedlings in both seed soaking and drenching methods. Colonization of bean seedlings by the bacterial endophytes, B19 and B53 resulted in the biocontrol of F. solani in planta, reduced disease severity and incidence, and significantly increased both root and shoot biomass compared to the control. Taxonomic identification using 16S rRNA revealed that the two isolates belong to Enterobacter hormaechei subsp., Xiangfangensis and Bacillus megaterium. Our results demonstrate the potential use of these two isolates in the biocontrol of the bean root rot pathogen, F. solani and plant growth promotion.

Diversity of endophytic bacteria in wild rice (Oryza meridionalis) and potential for promoting plant growth and degrading phthalates

Phthalates (PAEs) accumulated in agricultural soils and rice have increased human exposure risks. Microbial degradation could efficiently reduce the residue of organic pollutants in soil and crop plants. Here, we hypothesized that endophytic bacteria from wild rice have the potential for degradation of PAEs and plant growth promoting. The endophytic bacterial community and functional diversity in wild rice (Oryza meridionalis) were analyzed for the first time, and the potential for PAE degradation and plant growth promoting by endophytes were investigated. The results of Illumina high-throughput sequencing revealed that abundant endophytes inhabited in wild rice with Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria being the dominant phyla. Endophytic bacterial diversity and complexity were confirmed by isolation and clustering of isolates. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that endophytes exerted diverse functions such as plant growth promoting, xenobiotics biodegradation, pollution remediation and bacterial chemotaxis. Pure culture experiment showed that 30 isolated endophytic strains exhibited in vitro plant growth promoting activities, and rice plants inoculated with these strains confirmed their growth promoting abilities. Some endophytic strains were capable of efficiently degrading PAEs, with the highest removal percentage of di-n-butyl phthalate (DBP) up to 96.1% by Bacillus amyloliquefaciens strain L381 within 5 days. Synthetic community F and strain L381 rapidly removed DBP from soil (removing 91.0%-99.2% within 10 d and from rice plant slurry (removing 93.4%-99.2% within 5 d). These results confirmed the hypothesis and demonstrated the diversity of endophytic bacteria in wild rice with diverse functions, especially for plant growth promoting and removing PAEs. These multifunctional endophytic bacteria provided good alternatives to reduce PAE accumulation in crops and increase yield.

Surface sterilization for isolation of endophytes: Ensuring what (not) to grow

Endophytic microbiota opens a magnificent arena of metabolites that served as a potential source of medicines for treating a variety of ailments and having prospective uses in agriculture, food, cosmetics, and many more. There are umpteen reports of endophytes improving the growth and tolerance of plants. In addition, endophytes from lifesaving drug-producing plants such as Taxus, Nothapodytes, Catharanthus, and so forth have the ability to produce host mimicking compounds. To harness these benefits, it is imperative to isolate the true endophytes, not the surface microflora. The foremost step in endophyte isolation is the removal of epiphytic microbes from plant tissues, called as surface sterilization. The success of surface sterilization decides "what to grow" (the endophytes) and "what not to grow" (the epiphytes). It is very crucial to use an appropriate sterilant solution, concentration, and exposure time to ensure thorough surface disinfection with minimal damage to the endophytic diversity. Commonly used surface sterilants include sodium hypochlorite (2%-10%), ethanol (70%-90%), mercuric chloride (0.1%), formaldehyde (40%), and so forth. In addition, the efficiency could further be improved by pretreatment with surfactants such as Triton X-100, Tween 80, and Tween 20. This review comprehensively deals with the various sterilants and sterilization methods for the isolation of endophytic microbes. In addition, the mechanisms and rationale behind using specific surface sterilants have also been elaborated at length.

Therapeutic prospects of endophytic Bacillus species from Berberis lycium against oxidative stress and microbial pathogens

Endophytes are microorganisms residing within plant tissues. Bacterial endophytes are important sources for production of pharmaceutically important metabolites. Berberis lycium is an important medicinal plant and there exist no report regarding isolation and determination of bioactive potential of its bacterial endophytes. Therefore the present study was aimed to isolate and identify bacterial endophytes from Berberis lycium. The study resulted in isolation of 20 strains of bacterial endophytes. Based on their antibacterial activity three strains were identified as Bacillus cereus (LBL6), Bacillus thuringiensis (SBL3) and Bacillus anthracis (SBL4) on basis of 16SrRNA gene using universal primers. Crude ethyl acetate extracts of LBL6, SBL3 and SBL4 were further evaluated for antioxidant and antifungal activities. Moderate antioxidant activity (56 %) at a concentration of 1000 µg/mL was observed for LBL6 followed by 45 and 43 % activity by SBL4 and SBL3 respectively. Significant antifungal activity was observed against Aspergillus niger (60 %) and Aspergillus flavus (56 %) at concentration of 4 mg/mL of SBL3 and SBL4 respectively. GCMS analysis of extract (LBL6) exhibited presence of 12 bioactive secondary metabolites corresponding to antimicrobial, antifungal, antioxidant, antitumor and anticancer activities. In conclusion, present study highlighted the importance of Berberis lycium to host diverse bacterial endophytes of pharmaceutical importance.

Functional and morphological analysis of isolates of phylloplane and rhizoplane endophytic bacteria interacting in different cocoa production systems in the Amazon

Endophytic bacteria colonize different internal tissues of plants without damaging their cells. They can establish themselves in the same niche as other microorganisms and develop antagonistic activities against phytopathogens. There is little research on the functional and morphological characterization of these bacteria in production systems in the Amazon. Thus, the objective of this work was to functionally and morphologically characterize endophytic bacteria isolated from cocoa trees (Theobroma cacao L.) and evaluate their antagonistic potential against phytopathogens. A total of 197 endophytic bacteria isolates were obtained from leaves and roots of cocoa plants with different production systems and at different times of the year. The characterization of functional groups consisted of proteolytic, amylolytic and cellulolytic activity and ability to fix nitrogen and solubilize phosphate. Morphological diversity was evaluated mainly according to the following parameters: shape, color, size and elevation of the colony. Thirteen isolates of endophytic bacteria, selected by cluster analysis, were used to evaluate the antagonistic potential in paired trials against four species of phytopathogenic fungi. The largest amount of endophytic bacteria was isolated from the root (95.9%), in the dry season. The most expressive activities with regards to the enzyme index were amylolytic (71.9%), proteolytic (70.2%) and nitrogen fixing (38.6%), respectively. The similarity analysis formed two clusters with isolates CS R 2.4 and CS R 2.25 exhibiting 100% similarity. Five isolates displayed inhibitory activity against phytopathogenic fungi, most notably isolate TS R 2.19, which exhibited antagonistic activity against all fungi and mycelial growth inhibition rates between 25.7% and 50.7%. Understanding the interaction between endophytes in cocoa plants is important as a possible additional tool in biological control. Our studies are incipient and the first to be carried out in different cocoa production systems in the state of Pará, Brazil.

Prospecting Endophytic Bacteria Endowed With Plant Growth Promoting Potential Isolated From Camellia sinensis

Endophytes are well-acknowledged inoculants to promote plant growth, and extensive research has been done in different plants. However, there is a lacuna about the endophytes associated with tea clones and their benefit to promote plant growth. The present study focuses on isolating and characterizing the beneficial endophytic bacteria (EnB) prevalent in commercially important tea clones cultivated in North Eastern India as plant growth promoters. Diversity of culturable EnB microbiome, in vitro traits for plant growth promotion (PGP), and applicability of potent isolates as bioinoculant for in vivo PGP abilities have been assessed in the present study. A total of 106 EnB identified as members of phyla Proteobacteria, Firmicutes, and Actinobacteria were related to 22 different genera and six major clusters. Regarding PGP traits, the percentage of isolates positive for the production of indole acetic acid, phosphate solubilization, nitrogen fixation siderophore, ammonia, and 1-aminocyclopropane-1-carboxylic acid deaminase production were 86.8, 28.3, 78.3, 30.2, 95.3, and 87.7, respectively. In total, 34.0, 52.8, and 17.0% of EnB showed notable production of hydrolytic enzymes like cellulase, protease, and amylase, respectively. Additionally, based on the bonitur score, the top two isolates K96 identified as Stenotrophomonas sp. and M45 identified as Pseudomonas sp. were evaluated for biofilm formation, motility, and in vivo plant growth promoting activity. Results suggested strong biofilm formation and motility in K96 and M45 which may attribute to the colonization of the strains in the plants. Further in vivo plant growth promotion experiment suggested sturdy efficacy of the K96 and M45 as plant growth promoters in nursery condition in commercial tea clones Tocklai vegetative (TV) TV22 and TV26. Thus, this study emphasizes the opportunity of commercialization of the selected isolates for sustainable development of tea and other crops.

Endophytes from African Rice (Oryza glaberrima L.) Efficiently Colonize Asian Rice (Oryza sativa L.) Stimulating the Activity of Its Antioxidant Enzymes and Increasing the Content of Nitrogen, Carbon, and Chlorophyll

Bacterial endophytes support the adaptation of host plants to harsh environments. In this study, culturable bacterial endophytes were isolated from the African rice Oryza glaberrima L., which is well-adapted to grow with poor external inputs in the tropical region of Mali. Among these, six N-fixer strains were used to inoculate O. glaberrima RAM133 and the Asian rice O. sativa L. cv. Baldo, selected for growth in temperate climates. The colonization efficiency and the N-fixing activity were evaluated and compared for the two rice varieties. Oryza sativa-inoculated plants showed a fairly good colonization efficiency and nitrogenase activity. The inoculation of Oryza sativa with the strains Klebsiella pasteurii BDA134-6 and Phytobacter diazotrophicus BDA59-3 led to the highest nitrogenase activity. In addition, the inoculation of ‘Baldo’ plants with the strain P. diazotrophicus BDA59-3 led to a significant increase in nitrogen, carbon and chlorophyll content. Finally, ‘Baldo’ plants inoculated with Kl. pasteurii BDA134-6 showed the induction of antioxidant enzymes activity and the maintenance of nitrogen-fixation under salt stress as compared to the unstressed controls. As these endophytes efficiently colonize high-yielding crop varieties grown in cold temperate climates, they become good candidates to promote their growth under unfavorable conditions.

Screening of sunflower associated bacteria as biocontrol agents for plant growth promotion

Deleterious effects of artificially applied chemicals have highlighted the significance of biocontrol agents as suitable substitute for sustainable agriculture. In present study, three endophytic bacterial strains SV7, SV10 and LV19 showed extensive range of antifungal as well as plant growth promoting activities signifying potential to accomplish the requirement. Phylogenetic analysis revealed 100% similarity of three strains with taxon Firmicute. However, there was division among these isolates on basis of subgroups as SV7 belonged to Exiguobacterium auranticum, SV10 belonged to Paenibacillus sp. and LV19 was best fit in subgroup Priestia koreensis. All strains showed antifungal activity against Fusarium oxysporum on three different media (PDA, NA, LA) with maximum activity (53%) of LV19 strain on NA and least activity (13%) on PDA medium as recorded by zones of inhibition. In growth promotion experiments, combination of LV19 with Fusarium significantly suppressed chances of Fusarium wilt which is commonly caused by Fusarium oxysporum in sunflower plants. Diverse growth parameters (seed germination percentage, lengths and fresh weights of root and shoot) were significantly increased from 34 to 909% over pathogen infected plants only which was further proved by their root colonization analysis. Based on most efficient growth promotion by LV19 strain, expression of five plant defense related genes (SOD, PAL, NPR1, PR5, Chitinase) was evaluated revealing enhanced expression by 1.7-270-folds in consortium of LV19 and Fusarium. Thus, current study provided a scientific justification that bacterial strains in specific LV19 (Priestia koreensis) could be further developed as biocontrol agent with potential of plant growth promotion.

Antifungal activity and molecular docking of phenol, 2,4-bis(1,1-dimethylethyl) produced by plant growth-promoting actinobacterium Kutzneria sp. strain TSII from mangrove sediments

The present study reveals the plant growth-promoting (PGP) potentials and characterizes the antifungal metabolites of Kutzneria sp. strain TSII isolated from mangrove sediment soil through in vitro and in silico studies. In this study, Kutzneria sp. strain TSII was screened for PGP activities and the antifungal activities against Pithomyces atro-olivaceous, a leaf spot-associated pathogen in groundnut plants. The ethyl acetate extract of Kutzneria sp. strain TSII was purified using column chromatography, and the presence of various antimicrobial compounds was studied by gas chromatography-mass spectrometry (GC-MS) analysis. In silico modeling and docking were carried out to evaluate the antifungal potent of bioactive compound. Kutzneria sp. strain TSII produced proteases, phosphatases, ammonia, siderophores, cellulases, indole acetic acid (IAA), lipases, and amylases, indicating its ability to enhance the growth of plants. The ethyl acetate extract of Kutzneria sp strain TSII was found to be a potent inhibitor of fungal mycelial growth in the potato dextrose agar (PDA) plates. The GC-MS spectral study showed 24 antimicrobial compounds belonging to five chemical groups: phenolics, phthalates, fatty acid methyl esters (FAME), spiro, and fatty alcohols. In silico docking studies showed that phenol, 2,4-bis(1,1-dimethylethyl)-effectively attaches with the active site of mitochondrial F₁F₀ Adenosine triphosphate synthase enzymes of Pithomyces atro-olivaceous. Hence, it is clear that these antifungal compounds shall be formulated shortly to treat many plant fungal diseases in an eco-friendly manner.

Changes in Bacterial Endophyte Community Following Aspergillus flavus Infection in Resistant and Susceptible Maize Kernels

Aspergillus flavus (A. flavus)-mediated aflatoxin contamination in maize is a major global economic and health concern. As A. flavus is an opportunistic seed pathogen, the identification of factors contributing to kernel resistance will be of great importance in the development of novel mitigation strategies. Using V3–V4 bacterial rRNA sequencing and seeds of A. flavus-resistant maize breeding lines TZAR102 and MI82 and a susceptible line, SC212, we investigated kernel-specific changes in bacterial endophytes during infection. A total of 81 bacterial genera belonging to 10 phyla were detected. Bacteria belonging to the phylum Tenericutes comprised 86–99% of the detected phyla, followed by Proteobacteria (14%) and others (<5%) that changed with treatments and/or genotypes. Higher basal levels (without infection) of Streptomyces and Microbacterium in TZAR102 and increases in the abundance of Stenotrophomonas and Sphingomonas in MI82 following infection may suggest their role in resistance. Functional profiling of bacteria using 16S rRNA sequencing data revealed the presence of bacteria associated with the production of putative type II polyketides and sesquiterpenoids in the resistant vs. susceptible lines. Future characterization of endophytes predicted to possess antifungal/ anti-aflatoxigenic properties will aid in their development as effective biocontrol agents or microbiome markers for maize aflatoxin resistance.

Antagonistic Activity of Bacteria Isolated from the Periplaneta americana L. Gut against Some Multidrug-Resistant Human Pathogens

The insect gut is home to a wide range of microorganisms, including several bacterial species. Such bacterial symbionts provide various benefits to their insect hosts. One of such services is providing metabolites that resist infections. Little data are available about gut-inhabiting bacteria for several insect groups. Through the present work, the gut bacteria associated with the American cockroach (Periplaneta americana L.) were isolated, identified, and studied for their potential antimicrobial activity against multidrug-resistant (MDR) human pathogens. The cockroaches were collected from three different environmental sites. Gut bacteria were isolated, and sixteen species of bacteria were identified using Vitek MALDI-TOF MS. The antagonistic activity of the identified bacteria was tested against a panel of multidrug-resistant bacteria and fungi, namely: methicillin-resistant Staphylococcus aureus (MRSA) (clinical isolate), Streptococcus mutans Clarke (RCMB 017(1) ATCC ^® 25175™) (Gram-positive bacteria), Enterobacter cloacae (RCMB 001(1) ATCC^® 23355™) and Salmonella enterica (ATCC^® 25566™) (Gram-negative bacteria). The isolates were also tested against human pathogenic fungi such as Candida albicans (RCMB005003(1) ATCC^® 10231™), Aspergillus niger (RCMB002005), Aspergillus fumigatus (RCMB002008), Aspergillus flavus (RCMB002002), and Penicillium italicum (RCMB 001018(1) IMI193019). The results indicated that some bacterial species from the cockroach gut could antagonize the growth activity of all the tested pathogens. Such antimicrobial properties could ultimately lead to the future development of therapeutic drugs. The evaluation and mode of action of antagonistic gut bacteria against the most affected MDR pathogens were demonstrated using transmission electron microscopy (TEM).

Revisiting Plant-Microbe Interactions and Microbial Consortia Application for Enhancing Sustainable Agriculture: A Review

The present scenario of agricultural sector is dependent hugely on the use of chemical-based fertilizers and pesticides that impact the nutritional quality, health status, and productivity of the crops. Moreover, continuous release of these chemical inputs causes toxic compounds such as metals to accumulate in the soil and move to the plants with prolonged exposure, which ultimately impact the human health. Hence, it becomes necessary to bring out the alternatives to chemical pesticides/fertilizers for improvement of agricultural outputs. The rhizosphere of plant is an important niche with abundant microorganisms residing in it. They possess the properties of plant growth promotion, disease suppression, removal of toxic compounds, and assimilating nutrients to plants. Utilizing such beneficial microbes for crop productivity presents an efficient way to modulate the crop yield and productivity by maintaining healthy status and quality of the plants through bioformulations. To understand these microbial formulation compositions, it becomes essential to understand the processes going on in the rhizosphere as well as their concrete identification for better utilization of the microbial diversity such as plant growth–promoting bacteria and arbuscular mycorrhizal fungi. Hence, with this background, the present review article highlights the plant microbiome aboveground and belowground, importance of microbial inoculants in various plant species, and their subsequent interactive mechanisms for sustainable agriculture.

Survival and Virulence of Listeria monocytogenes during Storage on Chocolate Liquor, Corn Flakes, and Dry-Roasted Shelled Pistachios at 4 and 23°C

ABSTRACT

The survival and virulence of Listeria monocytogenes was assessed during storage on three low-moisture foods (LMFs): chocolate liquor, corn flakes, and shelled, dry-roasted pistachios (water activity [aw] of 0.18, 0.27, and 0.20, respectively). The LMFs were inoculated with a four-strain cocktail of L. monocytogenes at 8 log CFU/g, dried, held until the aw stabilized, and then stored at 4°C and 25 to 81% relative humidity (RH) and at 23°C and 30 to 35% RH for at least 336 days. At 4°C, L. monocytogenes remained stable on the LMFs for at least 336 days. At 23°C, L. monocytogenes levels declined on the chocolate liquor, corn flakes, and pistachios at initial rates of 0.84, 0.88, and 0.32 log CFU/g/month, respectively. After 8 months at 23°C, L. monocytogenes levels on the chocolate liquor and corn flakes decreased to below the limit of detection (i.e., 0.48 log CFU/g). Relative populations of each strain were assessed before storage (i.e., day 0) and after 6 and 12 months of storage at 23 and 4°C, respectively. Generally, a decline in the relative level of the serotype 1/2a strain was observed during storage, coupled with the relative increase in other strains, depending on the LMF and storage temperature. The total viable populations of L. monocytogenes determined by the PMAxx quantitative PCR method after >12 months of storage at 4°C were significantly (1.8- to 3.7-log) higher than those obtained by plating on tryptic soy agar with yeast extract. Decreases in the culturable population of L. monocytogenes during storage on the LMFs were the result of both cellular inactivation and transition to a viable-but-nonculturable state. The surviving cells, specifically after long-term storage at 4°C on the chocolate liquor and pistachios, remained infectious and capable of intracellular replication in Caco-2 enterocytes. These results are relevant for predictive modeling used in microbial health risk assessments and support the addition of LMFs to food safety questionnaires conducted during listeriosis outbreaks.

HIGHLIGHTS

Unlocking the potential of plant growth-promoting rhizobacteria on soil health and the sustainability of agricultural systems

The concept of soil health refers to specific soil properties and the ability to support and sustain crop growth and productivity, while maintaining long-term environmental quality. The key components of healthy soil are high populations of organisms that promote plant growth, such as the plant growth promoting rhizobacteria (PGPR). PGPR plays multiple beneficial and ecological roles in the rhizosphere soil. Among the roles of PGPR in agroecosystems are the nutrient cycling and uptake, inhibition of potential phytopathogens growth, stimulation of plant innate immunity, and direct enhancement of plant growth by producing phytohormones or other metabolites. Other important roles of PGPR are their environmental cleanup capacities (soil bioremediation). In this work, we review recent literature concerning the diverse mechanisms of PGPR in maintaining healthy conditions of agricultural soils, thus reducing (or eliminating) the toxic agrochemicals dependence. In conclusion, this review provides comprehensive knowledge on the current PGPR basic mechanisms and applications as biocontrol agents, plant growth stimulators and soil rhizoremediators, with the final goal of having more agroecological practices for sustainable agriculture.

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.

Plants endophytes: unveiling hidden agenda for bioprospecting toward sustainable agriculture

Endophytic microbes are present in nearly all of the plant species known to date but how they enter and flourish inside a host plant and display multiple benefits like plant growth promotion (PGP), biodegradation, and stress alleviation are still unexplored. Until now, the majority of the research has been conducted assuming that the host-endophyte interaction is analogous to the PGP microbes, although, studies related to the mechanisms of their infection, colonization as well as conferring important traits to the plants are limited. It would be fascinating to explore the role of these endophytic microbes in host gene expression, metabolism, and the modulation of phenotypic traits, under abiotic and biotic stress conditions. In this review, we critically focused on the following areas: (i) endophytic lifestyle and the mechanism of their entry into plant tissues, (ii) how endophytes modulate the immune system of plants and affect the genotypic and phenotypic expression of host plants under abiotic and biotic stress condition, and (iii) the role of omics and other integrated genomic approaches in unraveling complex host-endophyte signaling crosstalk. Furthermore, we discussed their role in phytoremediation of heavy metal stress and whole genomic analysis based on an understanding of different metabolic pathways these endophytes utilize to combat stress.

Quorum Quenching in a Novel Acinetobacter sp. XN-10 Bacterial Strain against Pectobacterium carotovorum subsp. carotovorum

Quorum sensing (QS) is a cell density-dependent mechanism that regulates the expression of specific genes in microbial cells. Quorum quenching (QQ) is a promising strategy for attenuating pathogenicity by interfering with the QS system of pathogens. N-Acyl-homoserine lactones (AHLs) act as signaling molecules in many Gram-negative bacterial pathogens and have received wide attention. In this study, a novel, efficient AHL-degrading bacterium, Acinetobacter sp. strain XN-10, was isolated from agricultural contaminated soil and evaluated for its degradation efficiency and potential use against QS-mediated pathogens. Strain XN-10 could effectively degrade N-(3-oxohexanoyl)-L-homoserine lactone (OHHL), N-hexanoyl-L-homoserine lactone (C6HSL), N-(3-oxododecanoyl)-L-homoserine lactone (3OC12HSL), and N-(3-oxooctanoyl)-L-homoserine lactone (3OC8HSL), which all belong to the AHL family. Analysis of AHL metabolic products by gas chromatography-mass spectrometry (GC-MS) led to the identification of N-cyclohexyl-propanamide, and pentanoic acid, 4-methyl, methyl ester as the main intermediate metabolites, revealing that AHL could be degraded by hydrolysis and dehydroxylation. All intermediates were transitory and faded away without any non-cleavable metabolites at the end of the experiment. Furthermore, strain XN-10 significantly attenuated the pathogenicity of Pectobacterium carotovorum subsp. carotovorum (Pcc) to suppress tissue maceration in carrots, potatoes, and Chinese cabbage. Taken together, our results shed light on the QQ mechanism of a novel AHL-degrading bacterial isolate, and they provide useful information which show potential for biocontrol of infectious diseases caused by AHL-dependent bacterial pathogens.

Characterization and bioremediation potential of nickel-resistant endophytic bacteria isolated from the wetland plant Tamarix chinensis

Wetlands have been proposed as a sink for pollutants such as heavy metals. Wetland plants play a significant role in the phytoremediation of heavy metals. Here, we isolated and characterized three novel nickel (Ni)-resistant endophytic bacteria (NiEB) from the wetland plant Tamarix chinensis. The NiEB were identified as Stenotrophomonas sp. S20, Pseudomonas sp. P21 and Sphingobium sp. S42. All isolates tolerated 50 mg L−1 Ni, with isolates S20 and P21 being more tolerant to Ni at up to 400 mg L−1. Moreover, isolate S42 removed 33.7% of nickel sulfate from the water by forming white precipitates. The three isolates exhibited different plant growth-promoting (PGP) traits related to the production of indole acetic acid (IAA), siderophores and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. Phytotoxicity studies revealed that the growth of the wetland plants in a high Ni concentration (200 mg L−1) recovered after co-incubation with isolate S42. Overall, this study presents the first report of NiEB isolation from wetland plants and provides novel insights into the diverse functions of endophytic bacteria in a plant host with the potential to improve Ni phytoremediation.

Drought-tolerant and plant growth-promoting endophytic Staphylococcus sp. having synergistic effect with silicate supplementation

Endophytic bacteria have been reported to have symbiotic, mutualistic, commensalistic or trophobiotic relationships with various plant parts. As part of its adaptation, many endophytic organisms are known to exhibit properties with multiple beneficial effects to the plant system. Even though many bacterial genera have been identified to have endophytic association, isolation of those which were previously demonstrated well for human association is quite interesting. In the study, endophytic bacteria Ceb1 isolated from the rhizome of Curcuma longa was identified by 16S rDNA sequencing as Staphylococcus sp. Further, Ceb1 was observed to have the ability to tolerate drought stress. While screening for the plant growth-promoting traits, Ceb1 was found to be positive for IAA production both under drought-stressed and normal conditions as confirmed by HPLC. The Ceb1 priming with Vigna unguiculata was observed to enhance the growth parameters of the plant. Analysis of Ceb1-treated plants by ICP-MS further showed modulation of both macro- and micronutrients. Upon drought stress induction in Vigna unguiculata, Ceb1 was found to provide synergistic plant growth-promoting effect to the plant along with the supplemented silicate sources. Under the changing agroclimatic conditions, exploring the plant stress-alleviating effects of endophytes is highly significant.

Isolation and characterization of Bacillus subtilis strain 1-L-29, an endophytic bacteria from Camellia oleifera with antimicrobial activity and efficient plant-root colonization

Endophytic bacteria, which are common in plant tissues, may help to control plant pathogens and enhance plant growth. Camellia oleifera, an oil-producing plant, is widely grown in warm, subtropical, hilly regions in China. However, C. oleifera is strongly negatively affected by C. oleifera anthracnose, which is caused by Colletetrichum fructicola. To find a suitable biocontrol agent for C. oleifera anthracnose, 41 endophytes were isolated from the stems, leaves, and roots of C. oleifera. Bacterial cultures were identified based on analyses of 16S rDNA sequences; most strains belonged to the genus Bacillus. The antagonistic effects of these strains on C. fructicola were tested in vitro. In total, 16 strains inhibited C. fructicola growth, with B. subtilis strain 1-L-29 being the most efficient. Strain 1-L-29 demonstrated antagonistic activity against C. siamense, C. asianum, Fusarium proliferatum, Agaricodochium camellia, and Pseudomonas syringae. In addition, this strain produced indole acetic acid, solubilized phosphate, grew on N-free media, and produced siderophores. To facilitate further microecological studies of this strain, a rifampicin-resistant, green fluorescent protein (GFP)-labeled strain, 1-L-29gfp^r, was created using protoplast transformation. This plasmid had good segregational stability. Strain 1-L-29gfp^r was re-introduced into C. oleifera and successfully colonized root, stem, and leaf tissues. This strain remained at a stable concentration in the root more than 20 d after inoculation. Fluorescence microscopic analysis showed that strain 1-L-29gfp^r thoroughly colonized the root surfaces of C. fructicola as well as the root vascular tissues of Arabidopsis thaliana.

Isolation, Screening, and Characterization of Plant-Growth-Promoting Bacteria from Durum Wheat Rhizosphere to Improve N and P Nutrient Use Efficiency

The main goal of this paper was to select promising microorganisms which could potentially act as plant-growth-promoting bacteria (PGPB) for durum wheat of Foggia County. At this scope, a new statistical framework, based on multivariate analyses and the evaluation of the statistical distribution of each trait, was used. Four hundred and seventy-four isolates were isolated from the rhizosphere of durum wheat in Foggia County and preliminarily screened as a function of four target indices (ammonium production, siderophores production, P-solubilization, and nitrification). After this step, the number of strains was reduced and the remaining isolates were tested through a quantitative approach, to assess the production of IAA (indole acetic acid), P-mineralization, and nitrification. In this second step, the cut-off was based on the whole population trend by evaluating for each trait the medians and quartiles. As a result, 16 promising isolates were selected and identified by 16S rDNA sequencing (Bacillus, Pseudomonas, Stenotrophomonas, and Lysinibacillus). The last step of this research was a preliminary validation in a growth chamber on eight strains. As screening and simple indices, two quantitative measures were chosen. The main result was the selection of at least three isolates (6P, 20P, and 25A) for a future field validation. They increased biomass and height by respectively 50% and 25%.

Phosphate-solubilizing bacteria improve Agave angustifolia Haw. growth under field conditions

BACKGROUND

Phosphate-solubilizing bacteria (PSB) can be an environment-friendly strategy to improve crop production in low-phosphorus (P) or P-deficient soils. The effect of indigenous mixed inocula of PSB on Agave angustifolia Haw. growth was assessed. The four treatments evaluated were T1 (Pseudomonas luteola + Enterobacter sp.), T2 (Pseudomonas luteola + Bacillus sp.), T3 (Pseudomonas luteola + Acinetobacter sp.), and T4 (control); each was replicated 25 times using a completely randomized design during 12 months under rain-fed conditions. Additionally, P solubilization in vitro of the mixed inocula with three different sources of inorganic P was tested.

RESULTS

The mixed inocula were able to solubilize more P from tricalcium phosphate Ca₃ (PO₄ )₂ than from aluminum phosphate (AlPO₄ ) and iron phosphate (FePO₄ ). Relative to the control, T2 increased plant height by 22.9%, leaf dry weight by 391.4%, plant stem diameter by 49.6%, and root dry weight by 193.9%. The stem solid soluble content increased 50.0% with T1. Plant-available soil P increased 94.6% with T3 and 77.3% with T1. Soil alkaline phosphatase activity increased 85.9% with T1.

CONCLUSION

T2 was the mixed inoculum that most improved Agave angustifolia plant growth. The indigenous mixed inocula of PSB evaluated appears to be a practical and efficient option for promoting field growth of Agave angustifolia plants. However, further research is necessary to achieve a deeper understanding of the relationships between different PSB species and their effects on agave, which may reveal some of the mechanisms of the synergistic interactions that are involved in the promotion of plant growth. © 2019 Society of Chemical Industry.

Bacterial and Fungal Endophytes: Tiny Giants with Immense Beneficial Potential for Plant Growth and Sustainable Agricultural Productivity

The conventional means of achieving enhanced agricultural productivity are not ecologically balanced and sustainable. The excessive use of synthetic agrochemicals, declining soil nutrients, and water-use issues, amongst others, are threats to the ecosystem. Additionally, environmental degradation and an increasing global population that will reach 9 billion by 2030 are further considerations. These issues mean a decline in the volume of food resources available to feed the world. Therefore, sustainably increasing agricultural productivity is a necessity for restoring soil fertility, feeding the populace, and improving the ecosystem. A way to achieve this is by using eco-friendly microbial inoculants. Endophytes inhabit the tissues of plants asymptomatically without causing adverse effects. Bacterial and fungal endophytes benefit plants by promoting growth, suppressing pathogens, and improving the stress tolerance and immunity of plants. Despite this vital role played by endophytes in their interactions with host plants, there is still a paucity of relevant review data. More importantly, the prospective use of endophytes as an alternative to synthetic agrochemicals to ensure agro-ecological crop productivity has not been well reviewed in the literature. Therefore, this review sought to highlight the potential use of endophytic microbial resources to achieve enhancements in agro-food system crops in a sustainable manner.

Microbial characterization and fermentative characteristics of crop maize ensiled with unsalable vegetables

Incorporation of carrot or pumpkin at 0, 20 or 40% dry matter (DM-basis) with crop maize, with or without a silage inoculant was evaluated after 70 days ensiling for microbial community diversity, nutrient composition, and aerobic stability. Inclusion of carrots or pumpkin had a strong effect on the silage bacterial community structure but not the fungal community. Bacterial microbial richness was also reduced (P = 0.01) by increasing vegetable proportion. Inverse Simpson's diversity increased (P = 0.04) by 18.3% with carrot maize silage as opposed to pumpkin maize silage at 20 or 40% DM. After 70 d ensiling, silage bacterial microbiota was dominated by Lactobacillus spp. and the fungal microbiota by Candida tropicalis, Kazachstania humilis and Fusarium denticulatum. After 14 d aerobic exposure, fungal diversity was not influenced (P ≥ 0.13) by vegetable type or proportion of inclusion in the silage. Inoculation of vegetable silage lowered silage surface temperatures on day-7 (P = 0.03) and day-14 (P ≤ 0.01) of aerobic stability analysis. Our findings suggest that ensiling unsalable vegetables with crop maize can successfully replace forage at 20 or 40% DM to produce a high-quality livestock feed.

Drought tolerance improvement in plants: an endophytic bacterial approach

Climate change is a crucial issue among the serious emerging problems which got a global attention in the last few decades. With the climate change, worldwide crop production has been seriously affected by drought stress. In this regard, various technologies including traditional breeding and genetic engineering are used to cope with drought stress. However, the interactions between plants and endophytic bacteria emerged as an interesting era of knowledge that can be used for novel agriculture practices. Endophytic bacteria which survive within plant tissues are among the most appropriate technologies improving plant growth and yield under drought conditions. These endophytic bacteria live within plant tissues and release various phytochemicals that assist plant to withstand in harsh environmental conditions, i.e., drought stress. Their plant growth-promoting characteristics include nitrogen fixation, phosphate solubilization, mineral uptake, and the production of siderophore, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and various phytohormones. These plant growth promoting characteristics of endophytic bacteria improve root length and density, which lead to the enhance drought tolerance. In addition, plant-endophytic bacteria assist plant to withstand against drought stress by producing drought-tolerant substances, for instance, abscisic acid, indole-3-acetic acid, ACC deaminase, and various volatile compounds. Indirectly, endophytic bacteria also improve osmotic adjustment, relative water content, and antioxidant activity of inoculated plants. Altogether, these bacterial-mediated drought tolerance and plant growth-promoting processes continue even under severe drought conditions which lead to enhanced plant growth promotion and yield. The present review highlights a natural and environment-friendly strategy in the form of drought-tolerant and plant growth-promoting endophytic bacteria to improve drought tolerance in plants.

Culturable endophytic bacteria of Camellia species endowed with plant growth promoting characteristics

AIM

Tea (Camellia sinensis (L.) O. Kuntze) is an economically important caffeine-containing beverage crop with massive plantation in the Northeast corner of the agroclimatic belt of India. The main aim of the work was to isolate, identify and characterize the native plant growth promoting endophytes associated with tea for future microbe based bioformulation.

METHODS AND RESULTS

A total of 129 endophytic bacteria were isolated and characterized for plant growth promoting traits such as indole-3-acetic acid (IAA), phosphate solubilization, ammonia production, biocontrol traits like siderophore and extracellular enzyme production. BOX-PCR fingerprinting was used to differentiate the various bacterial isolates obtained from six different tea species. 16S rRNA sequencing and blast analysis showed that these isolates belonged to different genera, that is, Bacillus, Brevibacterium, Paenibacillus and Lysinibacillus. Lysinibacillus sp. S24 showed the highest phosphate solubilization and IAA acid production efficiency of 268·4 ± 14·3 and 13·5 ± 0·5 µg ml^-1 , respectively. Brevibacterium sp. S91 showed the highest ammonia production of 6·2 ± 0·5 µmol ml^-1 . Chitinase, cellulase, protease and pectinase activities were shown by 4·6, 34·1, 27·13 and 13·14% of the total isolates, respectively. Similarly, 41% of the total isolates were positive for 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity. Further, the potent PGP isolates, S24 and S91 were able to enhance the vegetative parameters such as dry/fresh weight of root and shoot of tea plants in nursery conditions.

CONCLUSION

Our findings corroborate that tea endophytic bacteria possess the potential to demonstrate multiple PGP traits both, in vivo and in vitro and have the potential for further large-scale trials.

SIGNIFICANCE AND IMPACT OF THE STUDY

The exploration of tea endophytic bacterial community is suitable for the development of bioformulations for an integrated nutrient management and thus sustainable crop production and decreasing the hazardous effects of chemical fertilizers on the environment and human health.

Inside the plant: addressing bacterial endophytes in biotic stress alleviation

Bacterial endophytes are the internal association of bacteria with the plants, cherished whole or any part of their life cycle inside the plant. They are reported to improve plant health against the biotic stresses via de novo synthesis of structural compounds and stimulation of plant immunity. They are found to be vital in development of host resistance against phytopathogens and capable in reducing and elimination of deleterious effects of plant pathogens. Fungal-, bacterial-, viral-, insect- and nematode-associated negative effect can be reduced by the bacterial endophytes. They are also reported to control plant pathogens through several defense mechanisms such as by producing antimicrobial compounds and antibiotics, de novo synthesis of structural compounds, keeping out of pathogens by niche competition and induction of plant immunity or induced systemic resistance. In this review, an effort is made to summarize the exploitation of endophytic bacteria as a biological substitute to control biotic stresses in agricultural practices.

Diversity and Functionality of Culturable Endophytic Bacterial Communities in Chickpea Plants

The aims of this study were to isolate, identify and characterize culturable endophytic bacteria from chickpea (Cicer arietinum L.) roots grown in different soils. In addition, the effects of rhizobial inoculation, soil and stress on the functionality of those culturable endophytic bacterial communities were also investigated. Phylogenetic analysis based on partial 16S rRNA gene sequences revealed that the endophytic bacteria isolated in this work belong to the phyla Proteobacteria, Firmicutes and Actinobacteria, with Enterobacter and Pseudomonas being the most frequently observed genera. Production of indoleacetic acid and ammonia were the most widespread plant growth-promoting features, while antifungal activity was relatively rare among the isolates. Despite the fact that the majority of bacterial endophytes were salt- and Mn-tolerant, the isolates obtained from soil with Mn toxicity were generally more Mn-tolerant than those obtained from the same soil amended with dolomitic limestone. Several associations between an isolate's genus and specific plant growth-promoting mechanisms were observed. The data suggest that soil strongly impacts the Mn tolerance of endophytic bacterial communities present in chickpea roots while rhizobial inoculation induces significant changes in terms of isolates' plant growth-promoting abilities. In addition, this study also revealed chickpea-associated endophytic bacteria that could be exploited as sources with potential application in agriculture.

Perspectives of Microbial Inoculation for Sustainable Development and Environmental Management

How to sustainably feed a growing global population is a question still without an answer. Particularly farmers, to increase production, tend to apply more fertilizers and pesticides, a trend especially predominant in developing countries. Another challenge is that industrialization and other human activities produce pollutants, which accumulate in soils or aquatic environments, contaminating them. Not only is human well-being at risk, but also environmental health. Currently, recycling, land-filling, incineration and pyrolysis are being used to reduce the concentration of toxic pollutants from contaminated sites, but too have adverse effects on the environment, producing even more resistant and highly toxic intermediate compounds. Moreover, these methods are expensive, and are difficult to execute for soil, water, and air decontamination. Alternatively, green technologies are currently being developed to degrade toxic pollutants. This review provides an overview of current research on microbial inoculation as a way to either replace or reduce the use of agrochemicals and clean environments heavily affected by pollution. Microorganism-based inoculants that enhance nutrient uptake, promote crop growth, or protect plants from pests and diseases can replace agrochemicals in food production. Several examples of how biofertilizers and biopesticides enhance crop production are discussed. Plant roots can be colonized by a variety of favorable species and genera that promote plant growth. Microbial interventions can also be used to clean contaminated sites from accumulated pesticides, heavy metals, polyaromatic hydrocarbons, and other industrial effluents. The potential of and key processes used by microorganisms for sustainable development and environmental management are discussed in this review, followed by their future prospects.