Biologic control ability of plant growth-promoting Paenibacillus lentimorbus NRRL B-30488 isolated from milk

Comparative genomic and functional analyses of Paenibacillus peoriae ZBSF16 with biocontrol potential against grapevine diseases, provide insights into its genes related to plant growth-promoting and biocontrol mechanisms

Paenibacillus peoriae is a plant growth-promoting rhizobacteria (PGPR) widely distributed in various environments. P. peoriae ZBFS16 was isolated from the wheat rhizosphere and significantly suppressed grape white rot disease caused by Coniella vitis. Here, we present the complete genome sequence of P. peoriae ZBFS16, which consists of a 5.83 Mb circular chromosome with an average G + C content of 45.62%. Phylogenetic analyses showed that ZBFS16 belongs to the genus P. peoriae and was similar to P. peoriae ZF390, P. peoriae HS311 and P. peoriae HJ-2. Comparative analysis with three closely related sequenced strains of P. peoriae identified the conservation of genes involved in indole-3-acetic acid production, phosphate solubilization, nitrogen fixation, biofilm formation, flagella and chemotaxis, quorum-sensing systems, two-component systems, antimicrobial substances and resistance inducers. Meanwhile, in vitro experiments were also performed to confirm these functions. In addition, the strong colonization ability of P. peoriae ZBFS16 was observed in soil, which provides it with great potential for use in agriculture as a PGPR. This study will be helpful for further studies of P. peoriae on the mechanisms of plant growth promotion and biocontrol.

Reducing Drought Stress in Plants by Encapsulating Plant Growth-Promoting Bacteria with Polysaccharides

Drought is a major abiotic stress imposed by climate change that affects crop production and soil microbial functions. Plants respond to water deficits at the morphological, biochemical, and physiological levels, and invoke different adaptation mechanisms to tolerate drought stress. Plant growth-promoting bacteria (PGPB) can help to alleviate drought stress in plants through various strategies, including phytohormone production, the solubilization of mineral nutrients, and the production of 1-aminocyclopropane-1-carboxylate deaminase and osmolytes. However, PGPB populations and functions are influenced by adverse soil factors, such as drought. Therefore, maintaining the viability and stability of PGPB applied to arid soils requires that the PGPB have to be protected by suitable coatings. The encapsulation of PGPB is one of the newest and most efficient techniques for protecting beneficial bacteria against unfavorable soil conditions. Coatings made from polysaccharides, such as sodium alginate, chitosan, starch, cellulose, and their derivatives, can absorb and retain substantial amounts of water in the interstitial sites of their structures, thereby promoting bacterial survival and better plant growth.

Comparing the growth-promoting potential of Paenibacillus lentimorbus and Bacillus amyloliquefaciens in Oryza sativa L. var. Sarju-52 under suboptimal nutrient conditions

An adequate supply of mineral nutrients is crucial to obtain optimum productivity in agriculture. The present investigation was carried to find the inoculation effect of plant growth-promoting rhizobacteria (PGPR), i.e., Paenibacillus lentimorbus B-30488 (B-30488), Bacillus amyloliquefaciens SN13 (SN13) and their consortium for the growth of rice var. Sarju-52, grown under suboptimal nutrient conditions. The study revealed that the individual PGPR treatments showed comparatively better performance than consortia in morphological, physiological, biochemical, and nutrient analysis. Towards understanding the complex mechanism(s), untargeted metabolite profiling was performed using GC-MS, showed alteration of metabolites in rice seedlings facing suboptimal nutrient conditions and inoculated with PGPR. Metabolites such as oleic acid, mannitol, and ethyl iso-allocol were accumulated significantly under starved conditions. Under suboptimal nutrient conditions, sugars such as ribose, glucose, fructose, trehalose, palmitic acid, and myristic acid were accumulated significantly in PGPR inoculated seedlings. The significantly altered pathways due to PGPR inoculation under suboptimal nutrient conditions mainly belongs to carbohydrate and fatty acid metabolism. Interestingly, it was observed that among all the treatments, inoculation with SN13 performed comparatively better than other treatments. Further, in SN13 inoculated samples the qRT-PCR analysis of transcription factors and metabolism-related genes were validated that indicates PGPR deploy metabolic re-programming in rice var. Sarju-52 to enhance its nutrient use efficiency, tolerance, and growth under suboptimum nutrient conditions.

Bacillus amyloliquefaciens inoculation alters physiology of rice (Oryza sativa L. var. IR-36) through modulating carbohydrate metabolism to mitigate stress induced by nutrient starvation

To avoid disproportionate usage of chemicals in agriculture, an alternative eco-friendly strategy is required to improve soil fertility, and enhance crop productivity. Therefore, the present study demonstrates the role of plant beneficial rhizobacteria viz., Paenibacillus lentimorbus B-30488 (B-30488), Bacillus amyloliquefaciens SN13 (SN13), and their consortium in rice (Oryza sativa L. var. IR-36) facing nutrient deprivation. Parameters such as proline, total soluble sugar, relative water content, electrolytic leakage and malondialdehyde content were modulated in control rice seedlings as compared to treated under nutrient starved conditions. Bacterial inoculation not only significantly improved the agronomic parameters but also concentrations, uptake and partitioning of macro-micro nutrients. To disclose PGPR induced mechanisms to low nutrient stress tolerance, GC-MS analysis was performed. Overall 43 differential metabolites were characterized. Proline, glutamine, linolenic acid, malic acid, ribitol, propanoic acid and serine were accumulated in seedlings exposed to nutrient starvation. In PGPR inoculated rice glucose, fructose, mannose, glucitol, oleic acid, gulonic acid, raffinose, inositol were accumulated that induce metabolic and physiological parameters to reduce the impact of stress. Based on results SN13 was selected for gene expression analysis of metabolism-related genes that further affirmed the ability of PGPR to modulate carbohydrate metabolism in rice seedlings under suboptimum nutrient level.

Low Temperature (15 °C) Reduces Bacterial Diversity and Prolongs the Preservation Time of Volvariella volvacea

Straw mushroom (Volvariella volvacea) is the most commonly cultivated edible fungus in the world, but the challenges associated with the preservation have limited its marketability. Microbiology, especially bacteria, play a key role in the deterioration of food, this study aimed to reveal the succession of the bacterial community on the surfaces of V. volvacea fruit bodies under different temperature conditions. We amplified 16S rRNA genes of V4 regions, obtained the bacterial species information by using high-throughput sequencing technology, and analyzed the effects of environmental temperature and preservation time on bacterial communities. The relative abundances of Firmicutes, Bacilli, and Bacillales increased significantly when straw mushrooms began to rot. Furthermore, the relative abundances of Paenibacillus, Lysinibacillus and Solibacillus, which belong to Bacillales, increased with the decay of straw mushroom. The Shannon and Simpson indices of V. volvacea stored at 30 °C were significantly higher than those of V. volvacea stored at 15 °C, which indicates that a high temperature contributes to the improvement in the species diversity. According to the linear discriminant analysis (LDA) effect size (LEfSe) results, the number of biomarkers in the 30 °C group (32, 42.11%) was significantly higher than that in the 15 °C group (17, 22.37%), indicating that a high temperature has a clustering effect on some bacterial communities. A Spearman correlation analysis showed that Pseudomonas, Stenotrophomonas and Solibacillus promoted the decay of straw mushroom. In conclusion, a high temperature increases the bacterial diversity on the straw mushroom surfaces and has a clustering effect on the bacterial communities. The bacterial community consisting of Firmicutes, Bacilli, Bacillales, Paenibacillus, Lysinibacillus, Pseudomonas, Stenotrophomonas and Solibacillus could promote the decay of straw mushroom, so new preservation materials research can focus on inhibiting anaerobic and decay-causing bacteria to prolong preservation time.

A multifaceted rhizobacterium Paenibacillus lentimorbus alleviates nutrient deficiency-induced stress in Cicer arietinum L

Nutrient deficiency in soil is one of the limiting factors responsible for stunted growth and poor flowering/fruiting of crops which result in decline in overall agricultural productivity. However, one important strategy to overcome the problem of nutrient deficiency and to avoid use of chemical fertilizers is the use of plant growth promoting rhizobacteria (PGPR). Paenibacillus lentimorbus NRRL B-30488 (hereafter B-30488), an efficient PGPR has been reported to have various plant growth promoting traits that help crops to mitigate various environmental stresses. Therefore, the present work was designed to examine the application of B-30488 on chickpea growth under nutrient stress condition. Plants inoculated with B-30488 showed positive modulation in physio-biochemical behaviour and mineral nutrient uptake for better growth and development. Alteration in gene expression and metabolic profile under nutrient stress condition in chickpea also supported the stress amelioration capability of B-30488. Principal component analysis statistically proved that improved growth performance of chickpea plants under nutrient stress was mainly due to B-30488 induced modulation of metabolic pathways. To the best of our knowledge, this is the first study for analysis of growth promotion and stress alleviation in chickpea plants subjected to nutrient stress in presence of PGPR B-30488.

Paenibacillus lentimorbus induces autophagy for protecting tomato from Sclerotium rolfsii infection

During biotic stress, plants use several mechanisms to protect themselves that include the production of reactive oxygen species (ROS), induction of pathogenesis-related proteins and cell death. Some plant growth promoting rhizobacteria (PGPR) are known to act as bio-control agents that protect crops against pathogens. The biocontrol activity of PGPR Paenibacillus lentimorbus (B-30488) against Sclerotium rolfsii showed previously where several defense-related genes were upregulated with ROS induction in tomato. We further evaluate the other possibility, i.e. role of autophagy in enhancing defense in tomato using PGPR. Confocal microscopy revealed the presence of an acidotropic dye Mono Dansyl Cadaverine (MDC) stained autophagosomes in B-30488 treated healthy and infected plants. These autophagosomes almost disappeared in plants treated with an autophagy inhibitor chloroquine. The results were also confirmed by ultrastructural analysis of leaf tissues using transmission electron microscopy. Enhanced expression of autophagy-related genes was also monitored in B-30488 primed fungal infected tissues as compared to control by qRT-PCR. Results of ROS accumulation, fluorescence, confocal and transmission electron microscopy and gene expression analysis revealed induction of autophagy using B-30488 as a biocontrol agent suggesting a role in enhancing disease resistance in tomato. Overall, the present study indicated a role of B-30488 as a biocontrol in enhancing disease resistance in tomato and also assists a better understanding of fungal pathogenesis that is expected to be useful in developing new strategies for disease control.

Combating Fusarium Infection Using Bacillus-Based Antimicrobials

Despite efforts to control toxigenic Fusarium species, wilt and head-blight infections are destructive and economically damaging diseases that have global effects. The utilization of biological control agents in disease management programs has provided an effective, safe, and sustainable means to control Fusarium-induced plant diseases. Among the most widely used microbes for biocontrol agents are members of the genus Bacillus. These species influence plant and fungal pathogen interactions by a number of mechanisms such as competing for essential nutrients, antagonizing pathogens by producing fungitoxic metabolites, or inducing systemic resistance in plants. The multivariate interactions among plant-biocontrol agent-pathogen are the subject of this study, in which we survey the advances made regarding the research on the Bacillus-Fusarium interaction and focus on the principles and mechanisms of action among plant-growth promoting Bacillus species. In particular, we highlight their use in limiting and controlling Fusarium spread and infestations of economically important crops. This knowledge will be useful to define strategies for exploiting this group of beneficial bacteria for use as inoculants by themselves or in combination with other microbes for enhanced crop protection.

Paenibacillus lentimorbus Inoculation Enhances Tobacco Growth and Extenuates the Virulence of Cucumber mosaic virus

Previous studies with Paenibacillus lentimorbus B-30488" (hereafter referred as B-30488), a plant growth promoting rhizobacteria (PGPR) isolated from cow's milk, revealed its capabilities to improve plant quality under normal and stress conditions. Present study investigates its potential as a biocontrol agent against an economically important virus, Cucumber mosaic virus (CMV), in Nicotiana tabacum cv. White Burley plants and delineates the physical, biophysical, biochemical and molecular perturbations due to the trilateral interactions of PGPR-host-CMV. Soil inoculation of B-30488 enhanced the plant vigor while significantly decreased the virulence and virus RNA accumulation by ~12 fold (91%) in systemic leaves of CMV infected tobacco plants as compared to the control ones. Histology of these leaves revealed the improved tissue's health and least aging signs in B-30488 inoculated tobacco plants, with or without CMV infection, and showed lesser intercellular spaces between collenchyma cells, reduced amount of xyloglucans and pectins in connecting primary cells, and higher polyphenol accumulation in hypodermis layer extending to collenchyma cells. B-30488 inoculation has favorably maneuvered the essential biophysical (ion leakage and photosynthetic efficiency) and biochemical (sugar, proline, chlorophyll, malondialdehyde, acid phosphatase and alkaline phosphatase) attributes of tobacco plants to positively regulate and release the virus stress. Moreover, activities of defense related enzymes (ascorbate peroxidase, guaiacol peroxidase, superoxide dismutase and catalase) induced due to CMV-infection were ameliorated with inoculation of B-30488, suggesting systemic induced resistance mediated protection against CMV in tobacco. The quantitative RT-PCR analyses of the genes related to normal plant development, stress and pathogenesis also corroborate well with the biochemical data and revealed the regulation (either up or down) of these genes in favor of plant to combat the CMV mediated stress. These improvements led tobacco plant to produce more flowers and seeds with no negative impact on plant health. The present study may advocate the applicability of B-30488 for crop yield improvement in virus infested areas.

Southern blight disease of tomato control by 1-aminocyclopropane-1-carboxylate (ACC) deaminase producing Paenibacillus lentimorbus B-30488

Tomato cultivation is highly susceptible for soil born diseases and among them southern blight disease caused by Scelerotium rolfsii is very common. For its management use of chemical fungicides is not very successful as their spores are able to survive for many years in the soil. As an alternative eco-friendly approach to control the disease antagonistic microbes are being characterized.Among them plant growth promoting rhizobacteria Paenibacillus lentimorbus B-30488 (B-30488) with antagonistic properties, multiple PGP attributes stress tolerance and ACC deaminase enzyme activity is characterized to decipher its mode of action against S. rolfsii under in vitro and in vivo conditions. In vitro results obtained from this study clearly demonstrate that B-30488 has ability to show antagonistic properties under different abiotic stresses against S. rolfsii. Similar results were also obtained from in vivo experiments where B-30488 inoculation has efficiently controlled the disease caused by S. rolfsii and improve the plant growth. Deleterious enhanced ethylene level in S. rolfsii infected plants was also ameliorated by inoculation of ACC deaminase producing B-30488. The ACC accumulation, ACO and ACS activities were also modulated in S. rolfsii infected plants. Results from defense enzymes and other biochemical attributes were also support the role of B-30488 inoculation in ameliorating the biotic stress caused by S. rolfsii in tomato plants. These results were further validated by pathogen related gene expression analysis by real time PCR. Overall results from the present study may be concluded that ACC deaminase producing B-30488 has ability to control the southern blight disease caused by S. rolfsii and commercial bioinoculant package may be developed.

Diversity of culturable bacterial endophytes of saffron in Kashmir, India

Saffron (Crocus sativus) is a medicinally important plant. The Kashmir valley (J&K, India) emblematizes one of the major and quality saffron producing areas in the world. Nonetheless, the area has been experiencing a declining trend in the production of saffron during the last decade. Poor disease management is one of the major reasons for declining saffron production in the area. Endophytes are known to offer control against many diseases of host plant. During the present study, culturable bacterial endophytes were isolated from saffron plant, identified and assessed for plant growth promoting activities. Molecular and phylogenetic analysis grouped the fifty-four bacterial isolates into eleven different taxa, viz. Bacillus licheniformis, B. subtilis, B. cereus, B. humi, B. pumilus, Paenibacillus elgii, B. safensis, Brevibacillus sp., Pseudomonas putida, Staphylococcus hominis and Enterobacter cloacae. The results were also supported with the identification based on BIOLOG system. B. licheniformis was the dominant endophyte in both leaves and corms of saffron. 81 % isolates showed lipase activity, 57 % cellulase, 48 % protease, 38 % amylase, 33 % chitinase and 29 % showed pectinase activity. 24 % of the isolates were phosphate solublizers, 86 % showed siderophore production and 80 % phytohormone production potential. The present repository of well characterized bacterial endophytes of saffron, have plant growth promoting potential which can be explored further for their respective roles in the biology of the saffron plant.

Salecan Enhances the Activities of β-1,3-Glucanase and Decreases the Biomass of Soil-Borne Fungi

Salecan, a linear extracellular polysaccharide consisting of β-1,3-D-glucan, has potential applications in the food, pharmaceutical and cosmetic industries. The objective of this study was to evaluate the effects of salecan on soil microbial communities in a vegetable patch. Compositional shifts in the genetic structure of indigenous soil bacterial and fungal communities were monitored using culture-dependent dilution plating, culture-independent PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR. After 60 days, soil microorganism counts showed no significant variation in bacterial density and a marked decrease in the numbers of fungi. The DGGE profiles revealed that salecan changed the composition of the microbial community in soil by increasing the amount of Bacillus strains and decreasing the amount of Fusarium strains. Quantitative PCR confirmed that the populations of the soil-borne fungi Fusarium oxysporum and Trichoderma spp. were decreased approximately 6- and 2-fold, respectively, in soil containing salecan. This decrease in the amount of fungi can be explained by salecan inducing an increase in the activities of β-1,3-glucanase in the soil. These results suggest the promising application of salecan for biological control of pathogens of soil-borne fungi.

Cooperative degradation of chitin by extracellular and cell surface-expressed chitinases from Paenibacillus sp. strain FPU-7

Chitin, a major component of fungal cell walls and invertebrate cuticles, is an exceedingly abundant polysaccharide, ranking next to cellulose. Industrial demand for chitin and its degradation products as raw materials for fine chemical products is increasing. A bacterium with high chitin-decomposing activity, Paenibacillus sp. strain FPU-7, was isolated from soil by using a screening medium containing α-chitin powder. Although FPU-7 secreted several extracellular chitinases and thoroughly digested the powder, the extracellular fluid alone broke them down incompletely. Based on expression cloning and phylogenetic analysis, at least seven family 18 chitinase genes were found in the FPU-7 genome. Interestingly, the product of only one gene (chiW) was identified as possessing three S-layer homology (SLH) domains and two glycosyl hydrolase family 18 catalytic domains. Since SLH domains are known to function as anchors to the Gram-positive bacterial cell surface, ChiW was suggested to be a novel multimodular surface-expressed enzyme and to play an important role in the complete degradation of chitin. Indeed, the ChiW protein was localized on the cell surface. Each of the seven chitinase genes (chiA to chiF and chiW) was cloned and expressed in Escherichia coli cells for biochemical characterization of their products. In particular, ChiE and ChiW showed high activity for insoluble chitin. The high chitinolytic activity of strain FPU-7 and the chitinases may be useful for environmentally friendly processing of chitin in the manufacture of food and/or medicine.