A phenazine-1-carboxylic acid producing polyextremophilic Pseudomonas chlororaphis (MCC2693) strain, isolated from mountain ecosystem, possesses biocontrol and plant growth promotion abilities

Roxarsone biotransformation by a nitroreductase and an acetyltransferase in Pseudomonas chlororaphis, a bacterium isolated from soil

Roxarsone (3-nitro-4-hydroxyphenylarsonic acid, Rox), a widely used organoarsenical feed additive, can enter soils and be further biotransformed into various arsenic species that pose human health and ecological risks. However, the pathway and molecular mechanism of Rox biotransformation by soil microbes are not well studied. Therefore, in this study, we isolated a Rox-transforming bacterium from manure-fertilized soil and identified it as Pseudomonas chlororaphis through morphological analysis and 16S rRNA gene sequencing. Pseudomonas chlororaphis was able to biotransform Rox to 3-amino-4-hydroxyphenylarsonic acid (3-AHPAA), N-acetyl-4-hydroxy-m-arsanilic acid (N-AHPAA), arsenate [As(V)], arsenite [As(III)], and dimethylarsenate [DMAs(V)]. The complete genome of Pseudomonas chlororaphis was sequenced. PcmdaB, encoding a nitroreductase, and PcnhoA, encoding an acetyltransferase, were identified in the genome of Pseudomonas chlororaphis. Expression of PcmdaB and PcnhoA in E. coli Rosetta was shown to confer Rox(III) and 3-AHPAA(III) resistance through Rox nitroreduction and 3-AHPAA acetylation, respectively. The PcMdaB and PcNhoA enzymes were further purified and functionally characterized in vitro. The kinetic data of both PcMdaB and PcNhoA were well fit to the Michaelis-Menten equation, and nitroreduction catalyzed by PcMdaB is the rate-limiting step for Rox transformation. Our results provide new insights into the environmental risk assessment and bioremediation of Rox(V)-contaminated soils.

Isolation and identification of pathogens of Morchella sextelata bacterial disease

Morel mushroom (Morchella spp.) is a rare edible and medicinal fungus distributed worldwide. It is highly desired by the majority of consumers. Bacterial diseases have been commonly observed during artificial cultivation of Morchella sextelata. Bacterial pathogens spread rapidly and cause a wide range of infections, severely affecting the yield and quality of M. sextelata. In this study, two strains of bacterial pathogens, named M-B and M-5, were isolated, cultured, and purified from the tissues of the infected M. sextelata. Koch's postulates were used to determine the pathogenicity of bacteria affecting M. sextelata, and the pathogens were identified through morphological observation, physiological and biochemical analyses, and 16S rRNA gene sequence analysis. Subsequently, the effect of temperature on the growth of pathogenic bacteria, the inhibitory effect of the bacteria on M. sextelata on plates, and the changes in mycelial morphology of M. sextelata mycelium were analyzed when M. sextelata mycelium was double-cultured with pathogenic bacteria on plates. The results revealed that M-B was Pseudomonas chlororaphis subsp. aureofaciens and M-5 was Bacillus subtilis. Strain M-B started to multiply at 10-15°C, and strain M-5 started at 15-20°C. On the plates, the pathogenic bacteria also produced significant inhibition of M. sextelata mycelium, and the observation of mycelial morphology under the scanning electron microscopy revealed that the inhibited mycelium underwent obvious drying and crumpling, and the healthy mycelium were more plump. Thus, this study clarified the pathogens, optimal growth environment, and characteristics of M. sextelata bacterial diseases, thereby providing valuable basic data for the disease prevention and control of Morchella production.

Pseudomonas PA14H7: Identification and Quantification of the 7-Hydroxytropolone Iron Complex as an Active Metabolite against Dickeya, the Causal Agent of Blackleg on the Potato Plant

Soft rot Pectobacteriaceae (SRP), such as Pectobacterium and Dickeya, are phytopathogenic agents responsible for blackleg disease on several crops, such as potatoes, affecting the yield and depressing the seed production quality. However, neither conventional nor biocontrol products are available on the market to control this disease. In this study Pseudomonas PA14H7, a bacteria isolated from potato rhizosphere, was selected as a potential antagonist agent against Dickeya solani. In order to understand the mechanism involved in this antagonism, we managed to identify the main active molecule(s) produced by PA14H7. Cell-free supernatant (CFS) of PA14H7 cultures were extracted and analyzed using LC-MS, GC-MS, and NMR. We further correlated the biological activity against Dickeya solani of extracted CFS-PA14H7 to the presence of 7-hydroxytropolone (7-HT) complexed with iron. In a second time, we have synthesized this molecule and determined accurately using LC-UV, LC-MS, and GC-MS that, after 48 h incubation, PA14H7 released, in its CFS, around 9 mg/L of 7-HT. The biological activities of CFS-PA14H7 vs. synthetic 7-HT, at this concentration, were evaluated to have a similar bacteriostatic effect on the growth of Dickeya solani. Even if 7-HT is produced by other Pseudomonas species and is mostly known for its antibacterial and antifungal activities, this is the first description of its involvement as an effective molecule against pectinolytic bacteria. Our work opens the way for the comprehension of the mode of action of PA14H7 as a biocontrol agent against potato blackleg.

Cold adapted Pseudomonas: ecology to biotechnology

The cold adapted microorganisms, psychrophiles/psychrotolerants, go through several modifications at cellular and biochemical levels to alleviate the influence of low temperature stress conditions. The low temperature environments depend on these cold adapted microorganisms for various ecological processes. The ability of the microorganisms to function in cold environments depends on the strategies directly associated with cell metabolism, physicochemical constrains, and stress factors. Pseudomonas is one among such group of microorganisms which is predominant in cold environments with a wide range of ecological and biotechnological applications. Bioformulations of Pseudomonas spp., possessing plant growth promotion and biocontrol abilities for application under low temperature environments, are well documented. Further, recent advances in high throughput sequencing provide essential information regarding the prevalence of Pseudomonas in rhizospheres and their role in plant health. Cold adapted species of Pseudomonas are also getting recognition for their potential in biodegradation and bioremediation of environmental contaminants. Production of enzymes and bioactive compounds (primarily as an adaptation mechanism) gives way to their applications in various industries. Exopolysaccharides and various biotechnologically important enzymes, produced by cold adapted species of Pseudomonas, are making their way in food, textiles, and pharmaceuticals. The present review, therefore, aims to summarize the functional versatility of Pseudomonas with particular reference to its peculiarities along with the ecological and biotechnological applications.

Multifaceted Impacts of Plant-Beneficial Pseudomonas spp. in Managing Various Plant Diseases and Crop Yield Improvement

The modern agricultural system has issues with the reduction of agricultural productivity due to a wide range of abiotic and biotic stresses. It is also expected that in the future the entire world population may rapidly increase and will surely demand more food. Farmers now utilize a massive quantity of synthetic fertilizers and pesticides for disease management and to increase food production. These synthetic fertilizers badly affect the environment, the texture of the soil, plant productivity, and human health. However, agricultural safety and sustainability depend on an ecofriendly and inexpensive biological application. In contrast to synthetic fertilizers, soil inoculation with plant-growth-promoting rhizobacteria (PGPR) is one of the excellent alternative options. In this regard, we focused on the best PGPR genera, Pseudomonas, which exists in the rhizosphere as well as inside the plant's body and plays a role in sustainable agriculture. Many Pseudomonas spp. control plant pathogens and play an effective role in disease management through direct and indirect mechanisms. Pseudomonas spp. fix the amount of atmospheric nitrogen, solubilize phosphorus and potassium, and also produce phytohormones, lytic enzymes, volatile organic compounds, antibiotics, and secondary metabolites during stress conditions. These compounds stimulate plant growth by inducing systemic resistance and by inhibiting the growth of pathogens. Furthermore, pseudomonads also protect plants during different stress conditions like heavy metal pollution, osmosis, temperature, oxidative stress, etc. Now, several Pseudomonas-based commercial biological control products have been promoted and marketed, but there are a few limitations that hinder the development of this technology for extensive usage in agricultural systems. The variability among the members of Pseudomonas spp. draws attention to the huge research interest in this genus. There is a need to explore the potential of native Pseudomonas spp. as biocontrol agents and to use them in biopesticide development to support sustainable agriculture.

Screening of natural phenazine producers for electroactivity in bioelectrochemical systems

Mediated extracellular electron transfer (EET) might be a great vehicle to connect microbial bioprocesses with electrochemical control in stirred-tank bioreactors. However, mediated electron transfer to date is not only much less efficient but also much less studied than microbial direct electron transfer to an anode. For example, despite the widespread capacity of pseudomonads to produce phenazine natural products, only Pseudomonas aeruginosa has been studied for its use of phenazines in bioelectrochemical applications. To provide a deeper understanding of the ecological potential for the bioelectrochemical exploitation of phenazines, we here investigated the potential electroactivity of over 100 putative diverse native phenazine producers and the performance within bioelectrochemical systems. Five species from the genera Pseudomonas, Streptomyces, Nocardiopsis, Brevibacterium and Burkholderia were identified as new electroactive bacteria. Electron discharge to the anode and electric current production correlated with the phenazine synthesis of Pseudomonas chlororaphis subsp. aurantiaca. Phenazine-1-carboxylic acid was the dominant molecule with a concentration of 86.1 μg/ml mediating an anodic current of 15.1 μA/cm² . On the other hand, Nocardiopsis chromatogenes used a wider range of phenazines at low concentrations and likely yet-unknown redox compounds to mediate EET, achieving an anodic current of 9.5 μA/cm² . Elucidating the energetic and metabolic usage of phenazines in these and other species might contribute to improving electron discharge and respiration. In the long run, this may enhance oxygen-limited bioproduction of value-added compounds based on mediated EET mechanisms.

Polyamine metabolizing rhizobacteria Pseudomonas sp. GBPI_506 modulates hormone signaling to enhance lateral roots and nicotine biosynthesis in Nicotiana benthamiana

Beneficial rhizobacteria in the soil are important drivers of plant health and growth. In this study, we provide the draft genome of a root colonizing and auxin-producing Pseudomonas sp. strain GBPI_506. The bacterium was investigated for its contribution in the growth of Nicotiana benthamiana (Nb) and biosynthesis of nicotine. The bacterium showed chemotaxis towards root exudates potentially mediated by putrescine, a polyamine compound, to colonize the roots of Nb. Application of the bacterium with the roots of Nb, increased plant biomass and total soluble sugars in the leaves, and promoted lateral root (LR) development as compared to the un-inoculated plants. Confocal analysis using transgenic (DR5:GFP) Arabidopsis showed increased auxin trafficking in the LR of inoculated plants. Upregulation of nicotine biosynthesis genes and genes involved in salicylic acid (SA) and jasmonic acid (JA) signaling in the roots of inoculated plants suggested increased nicotine biosynthesis as a result of bacterial application. An increased JA content in roots and nicotine accumulation in leaves provided evidence on JA-mediated upregulation of nicotine biosynthesis in the bacterized plants. The findings suggested that the bacterial root colonization triggered networking between auxin, SA, and JA to facilitate LR development leading to enhanced plant growth and nicotine biosynthesis in Nb.

Revisiting the oldest manure of India, Kunapajala: Assessment of its animal waste recycling potential as a source of plant biostimulant

India's oldest documented manure, most commonly referred to as Kunapajala, has a long history of over 1,000 years in crop cultivation. Kunapajala is primarily an in-situ decomposition technology of animal waste and can potentially provide an eco-friendly pipeline for recycling bio-waste into essential plant nutrients. This traditional animal manure, in addition, also contains dairy excreta (e.g., feces and urine), dairy products (e.g., milk and ghee), natural resources (e.g., honey), broken seeds or grains, and their non-edible by-product waste. Here, we aimed to assess the waste recycling and plant biostimulant potential of Kunapajala prepared from livestock (e.g., Black Bengal goats) or fish (e.g., Bombay duck) post-processed wastes over different decomposition periods, e.g., (0, 30, 60, and 90-days). In this study, an in-situ quantification of livestock- (lKPJ) and fish-based Kunapajala (fKPJ) reveals a dynamic landscape of essential plant primary nutrients, e.g., (0.70 > NH4-N < 3.40 g•L−1), (100.00 > P2O5 < 620.00 mg•L−1), and (175.00 > K2O < 340.00 mg•L−1), including other physico-chemical attributes of Kunapajala. Using correlation statistics, we find that the plant-available nutrient content of Kunapajala depicts a significant (p < 0.0001) transformation over decomposition along with microbial dynamics, abundance, and diversities, delineating a microbial interface to animal waste decomposition and plant growth promotion. Importantly, this study also reports the indole 3-acetic acid (IAA) content (40.00 > IAA < 135.00 mg•L−1) in Kunapajala. Furthermore, the bacterial screening based on plant growth-promoting traits and their functional analyses elucidate the mechanism of the plant biostimulant potential of Kunapajala. This assay finally reports two best-performing plant growth-promoting bacteria (e.g., Pseudomonas chlororaphis and Bacillus subtilis) by the 16S ribotyping method. In support, in-planta experiments have demonstrated, in detail, the bio-stimulative effects of Kunapajala, including these two bacterial isolates alone or in combination, on seed germination, root-shoot length, and other important agronomic, physio-biochemical traits in rice. Together, our findings establish that Kunapajala can be recommended as a source of plant biostimulant to improve crop quality traits in rice. Overall, this work highlights Kunapajala, for the first time, as a promising low-cost microbial technology that can serve a dual function of animal waste recycling and plant nutrient recovery to promote sustainable intensification in agroecosystems.

Salt tolerant PGPR strain Priestia endophytica SK1 promotes Fenugreek growth under salt stress by inducing nitrogen assimilation and secondary metabolites

AIMS

Soil salinity is a huge obstacle in crop production worldwide. Saline soil can reduce active chemical contents in medicinal plants of Leguminosae family through crippled normal nodule function. Intensive efforts are underway to improve yield and medicinal value of leguminous herbs under salt stress condition by using benign microbes. Here, an attempt was made to explore the salt tolerant bacteria associated with rhizosphere of fenugreek plant (Trigonella foenum-graecum L.) and to evaluate their impact on host plant growth and metabolite of pharmaceutical importance.

METHODS AND RESULTS

A salt tolerant plant growth promoting rhizobacterial (PGPR) strain Priestia endophytica SK1 isolated from fenugreek rhizospheric soil, which increased biomass and metabolite content in plants grown under saline stress. SK1 bacterial application induced nodule formation and enhanced nitrogen and phosphorus content under salt (100 mM NaCl) stress as compared to control plants. H2O2 production and lipid peroxidation as a measure of stress were observed high in control plants, while a reduction in these parameters was observed in plants inoculated with SK1. In addition, a significant effect was found on the phenolic compounds and trigonelline content in fenugreek plant inoculated with SK1 bacterium. An increased trigonelline content of about 54% over uninoculated control was recorded under salt stress.

CONCLUSION

The results of this study revealed that application of salt tolerant PGPR strain P. endophytica SK1 induced nitrogen fixation machinery that leads to alleviate salt stress and improved the biosynthesis of trigonelline content in fenugreek.

SIGNIFICANCE OF THE STUDY

This study extends our understanding on significance of rhizosphere microbiome and their beneficial role in plant health under environmental stress to promote agro-eco-farming practices.

Harnessing rhizobacteria to fulfil inter-linked nutrient dependency on soil and alleviate stresses in plants

Plant rhizo-microbiome comprises of complex microbial communities that colonizes at the interphase of plant roots and soil. Plant-growth-promoting rhizobacteria (PGPR) in the rhizosphere provides important ecosystem services ranging from release of essential nutrients for enhancing soil quality and improving plant health to imparting protection to plants against rising biotic and abiotic stresses. Hence, PGPR serve as restoring agents to rejuvenate soil health and mediate plant fitness in the facet of changing climate. Though, it is evident that nutrients availability in soil are managed through inter-linked mechanisms, how PGPR expediate these processes remain less recognized. Promising results of PGPR inoculation on plant growth are continually reported in controlled environmental conditions, however, their field application often fails due to competition with native microbiota and low colonization efficiency in roots. The development of highly efficient and smart bacterial synthetic communities by integrating bacterial ecological and genetic features provides better opportunities for successful inoculant formulations. This review provides an overview of the inter-play between nutrient availability and disease suppression governed by rhizobacteria in soil followed by the role of synthetic bacterial communities in developing efficient microbial inoculants. Moreover, an outlook on the beneficial activities of rhizobacteria in modifying soil characteristics to sustainably boost agroecosystem functioning is also provided.

An Evaluation of Aluminum Tolerant Pseudomonas aeruginosa A7 for In Vivo Suppression of Fusarium Wilt of Chickpea Caused by Fusarium oxysporum f. sp. ciceris and Growth Promotion of Chickpea

Chickpea wilt, caused by Fusarium oxysporum f. sp. ciceris, is a disease that decreases chickpea productivity and quality and can reduce its yield by as much as 15%. A newly isolated, moss rhizoid-associated Pseudomonas aeruginosa strain A7, demonstrated strong inhibition of Fusarium oxysporum f. sp. ciceris growth. An in vitro antimicrobial assay revealed A7 to suppress the growth of several fungal and bacterial plant pathogens by secreting secondary metabolites and by producing volatile compounds. In an in vivo pot experiment with Fusarium wilt infection in chickpea, the antagonist A7 exhibited a disease reduction by 77 ± 1.5%, and significantly reduced the disease incidence and severity indexes. Furthermore, A7 promoted chickpea growth in terms of root and shoot length and dry biomass during pot assay. The strain exhibited several traits associated with plant growth promotion, extracellular enzymatic production, and stress tolerance. Under aluminum stress conditions, in vitro growth of chickpea plants by A7 resulted in a significant increase in root length and plant biomass production. Additionally, hallmark genes for antibiotics production were identified in A7. The methanol extract of strain A7 demonstrated antimicrobial activity, leading to the identification of various antimicrobial compounds based on retention time and molecular weight. These findings strongly suggest that the strain’s significant biocontrol potential and plant growth enhancement could be a potential environmentally friendly process in agricultural crop production.

Psychrophilic Bacterial Phosphate-Biofertilizers: A Novel Extremophile for Sustainable Crop Production under Cold Environment

Abiotic stresses, including low-temperature environments, adversely affect the structure, composition, and physiological activities of soil microbiomes. Also, low temperatures disturb physiological and metabolic processes, leading to major crop losses worldwide. Extreme cold temperature habitats are, however, an interesting source of psychrophilic and psychrotolerant phosphate solubilizing bacteria (PSB) that can ameliorate the low-temperature conditions while maintaining their physiological activities. The production of antifreeze proteins and expression of stress-induced genes at low temperatures favors the survival of such organisms during cold stress. The ability to facilitate plant growth by supplying a major plant nutrient, phosphorus, in P-deficient soil is one of the novel functional properties of cold-tolerant PSB. By contrast, plants growing under stress conditions require cold-tolerant rhizosphere bacteria to enhance their performance. To this end, the use of psychrophilic PSB formulations has been found effective in yield optimization under temperature-stressed conditions. Most of the research has been done on microbial P biofertilizers impacting plant growth under normal cultivation practices but little attention has been paid to the plant growth-promoting activities of cold-tolerant PSB on crops growing in low-temperature environments. This scientific gap formed the basis of the present manuscript and explains the rationale for the introduction of cold-tolerant PSB in competitive agronomic practices, including the mechanism of solubilization/mineralization, release of biosensor active biomolecules, molecular engineering of PSB for increasing both P solubilizing/mineralizing efficiency, and host range. The impact of extreme cold on the physiological activities of plants and how plants overcome such stresses is discussed briefly. It is time to enlarge the prospects of psychrophilic/psychrotolerant phosphate biofertilizers and take advantage of their precious, fundamental, and economical but enormous plant growth augmenting potential to ameliorate stress and facilitate crop production to satisfy the food demands of frighteningly growing human populations. The production and application of cold-tolerant P-biofertilizers will recuperate sustainable agriculture in cold adaptive agrosystems.

Plant Growth Promotion at Low Temperature by Phosphate-Solubilizing Pseudomonas Spp. Isolated from High-Altitude Himalayan Soil

Scarcity of arable land, limited soil nutrient availability, and low-temperature conditions in the Himalayan regions need to be smartly managed using sustainable approaches for better crop yields. Microorganisms, able to efficiently solubilize phosphate at low temperatures, provide an opportunity to promote plant growth in an ecofriendly way. In this study, we have investigated the ability of psychrotolerant Pseudomonas spp., isolated from high altitudes of Indian Himalaya to solubilize P at low temperature. Quantitative estimation of phosphate solubilization and production of relevant enzymes at two different temperatures (15 and 25 °C) was performed for 4 out of 11 selected isolates, namely, GBPI_506 (Pseudomonas sp.), GBPI_508 (Pseudomonas palleroniana), GBPI_Hb61 (Pseudomonas proteolytica), and GBPI_CDB143 (Pseudomonas azotoformans). Among all, isolate GBPI_CDB143 showed highest efficiency to solubilize tri-calcium phosphate (110.50 ± 3.44 μg/mL) at 25 °C after 6 days while the culture supernatants of isolate GBPI_506 displayed the highest phytase activity (15.91 ± 0.35 U/mL) at 15 °C and alkaline phosphatase (3.09 ± 0.07 U/mL) at 25 °C in 6 and 9 days, respectively. Out of five different organic acids quantified, oxalic acid and malic acid were produced in maximum quantity by all four isolates. With the exception of GBPI_508, inoculation of bacteria promoted overall growth (rosette diameter, leaf area, and biomass) of Arabidopsis thaliana plants as compared to uninoculated control plants in growth chamber conditions. The plant growth promotion by each bacterial isolate was further validated by monitoring root colonization in the inoculated plants. These bacterial isolates with low-temperature phosphate solubilization potential along with phosphatases and phytase activity at low temperature could be harnessed for sustainable crop production in P-deficient agricultural soils under mountain ecosystems.

Biological Control of Take-All and Growth Promotion in Wheat by Pseudomonas chlororaphis YB-10

Wheat is a worldwide staple food crop, and take-all caused by Gaeumannomyces graminis var. tritici can lead to a tremendous decrease in wheat yield and quality. In this study, strain YB-10 was isolated from wheat rhizospheric soil and identified as Pseudomonas chlororaphis by morphology and 16S rRNA gene sequencing. Pseudomonas chlororaphis YB-10 had extracellular protease and cellulase activities and strongly inhibited the mycelium growth of Gaeumannomyces graminis var. tritici in dual cultures. Up to 87% efficacy of Pseudomonas chlororaphis YB-10 in controlling the take-all of seedlings was observed in pot experiments when wheat seed was coated with the bacterium. Pseudomonas chlororaphis YB-10 was also positive for indole acetic acid (IAA) and siderophore production, and coating wheat seed with the bacterium significantly promoted the growth of seedlings at 107 and 108 CFU/mL. Furthermore, treatment with Pseudomonas chlororaphis YB-10 increased activities of the wheat defense-related enzymes POD, SOD, CAT, PAL and PPO in seedlings, indicating induced resistance against pathogens. Overall, Pseudomonas chlororaphis YB-10 is a promising new seed-coating agent to both promote wheat growth and suppress take-all.

Arnebia euchroma, a Plant Species of Cold Desert in the Himalayas, Harbors Beneficial Cultivable Endophytes in Roots and Leaves

The endophytic mutualism of plants with microorganisms often leads to several benefits to its host including plant health and survival under extreme environments. Arnebia euchroma is an endangered medicinal plant that grows naturally in extreme cold and arid environments in the Himalayas. The present study was conducted to decipher the cultivable endophytic diversity associated with the leaf and root tissues of A. euchroma. A total of 60 bacteria and 33 fungi including nine yeasts were isolated and characterized at the molecular level. Among these, Proteobacteria was the most abundant bacterial phylum with the abundance of Gammaproteobacteria (76.67%) and genus Pseudomonas. Ascomycota was the most abundant phylum (72.73%) dominated by class Eurotiales (42.42%) and genus Penicillium among isolated fungal endophytes. Leaf tissues showed a higher richness (S_chao1) of both bacterial and fungal communities as compared to root tissues. The abilities of endophytes to display plant growth promotion (PGP) through phosphorus (P) and potassium (K) solubilization and production of ACC deaminase (ACCD), indole acetic acid (IAA), and siderophores were also investigated under in vitro conditions. Of all the endophytes, 21.51% produced ACCD, 89.25% solubilized P, 43.01% solubilized K, 68.82% produced IAA, and 76.34% produced siderophores. Six bacteria and one fungal endophyte displayed all the five PGP traits. The study demonstrated that A. euchroma is a promising source of beneficial endophytes with multiple growth-promoting traits. These endophytes can be used for improving stress tolerance in plants under nutrient-deficient and cold/arid conditions.

Phenazine-1-carboxylic acid (PCA) produced by Paraburkholderia phenazinium CK-PC1 aids postgermination growth of Xyris complanata seedlings with germination induced by Penicillium rolfsii Y-1

Symbiosis of Penicillium rolfsii Y-1 is essential for the seed germination of Hawaii yellow-eyed grass (Xyris complanata). However, the local soil where the plants grow naturally often suppresses the radicle growth of the seedlings. This radicle growth was drastically restored by coinoculation of Paraburkholderia phenazinium isolate CK-PC1, which is a rhizobacterium of X. complanata. It was found that the isolate CK-PC1 produced phenazine-1-carboxylic acid (PCA, 1) as a major metabolite. The biological effects of PCA (1) were investigated using the seeds of X. complanata and Mung bean (Vigna radiata) and it was uncovered that the symbiosis of the isolate CK-PC1was essential for the postgermination growth of X. complanata and the metabolite PCA (1) might partially contribute to promote the growth of the plants.

Elucidation and Identification of an Antifungal Compound from Pseudomonas aeruginosa DA3.1 Isolated from Soil in Vietnam

Background: Fusarium sp. and Rhizoctonia sp. fungi have been always threats to short-term crops. In Vietnam, corn and soybean suffer serious losses annually. Therefore, it is necessary to utilize an environmentally friendly antifungal compound that is highly effective against phytopathogenic fungi. Pseudomonas sp. is a popular soil bacterial strain and well known for its high antifungal activity. Objectives: This study was carried out to evaluate and assess the antifungal activity of a local bacterial strain namely DA3.1 that was later identified as Pseudomonas aeruginosa. This would be strong scientific evidence to develop an environmentally friendly biocide from a local microorganism strain for commercial use. Methods: The antifungal compound was purified from ethyl acetate extraction of deproteinized cell culture broth by a silica gel column (CH2Cl2/MeOH (0% - 10% MeOH)). The purity of the isolated compound was determined by HPLC, and its molecular structure was elucidated using spectroscopic experiments including one-dimensional (1D) (1H NMR, 13C NMR, DEPT) and two-dimensional (2D) (HMBC and HSQC) spectra. The activity of the purified compound against Fusarium sp. and Rhizoctonia sp. fungi was measured using the PDA-disk diffusion method, and its growth-promoting ability was evaluated using the seed germination test of corn and soybean. Results: The results showed that the antifungal compound produced by Pseudomonas aeruginosa DA3.1 had a retention factor (Rf) of 0.86 on thin layer chromatography (TLC). Based on the evidence of spectral data including proton nuclear magnetic resonance (1H NMR), carbon nuclear magnetic resonance (13C NMR), distortionless enhancement by polarization transfer (DEPT), heteronuclear multiple bond correlation (HMBC), and heteronuclear single quantum coherence (HSQC), the chemical structure was elucidated as phenazine-1-carboxylic. The purified compound showed inhibitory activity against F. oxysporum and R. solani and exhibited the ability of the germination of corn and soybean seeds. The results revealed the benefit of native P. aeruginosa DA3.1 and phenazine-1-carboxylic acid for use as a biocontrol agent, as well as a plant growth promoter. Conclusions: The antifungal compound isolated from local Pseudomonas DA3.1 was identified as phenazine-1-carboxylic acid that posed high antifungal activity and was a plant germination booster.

Modulation of agriculturally useful rhamnolipid profile of Pseudomonas sp. K6 due to the supplementation with chitosan and gold nanoparticles

As rhizobacteria have extensively been studied for the production of compounds with biocontrol properties, methods to enhance its production are very important. In this study, nanotechnological method to modulate the rhamnolipid production by Pseudomonas sp. K6 has been demonstrated. For this, Pseudomonas sp. K6 was cultured with different concentrations of chitosan nanoparticles (CNPs) and gold nanoparticles (AuNPs). The rhamnolipid production was further analyzed by CTAB- methylene blue agar assay and also by LC-MS/MS analysis. From the LC-MS/MS result, induction of dirhamnolipid production in K6 could be confirmed when cultured with CNPs (1, 5 and 10 mg/mL) and AuNPs (10, 25, 50 and 100 µg/mL). The monorhamnolipid production by K6 was observed to get enhanced when the K6 culture was supplemented with 2.5 mg/mL CNPs and 10 µg/mL AuNPs. Also, in planta study confirmed the biocontrol ability of rhamnolipid as it suppressed the Sclerotium rolfsii infection in Vigna unguiculata plants. As the rhamnolipids have versatile applications in the agricultural field, the nano-based approach to enhance its production from the biocontrol organism is significant.

Fighting plant pathogens with cold-active microorganisms: biopesticide development and agriculture intensification in cold climates

Cold-adapted (CA) microorganisms (= psychrophiles or psychrotolerants) are key players of many ecological interactions in natural ecosystems. Some of them can colonize the rhizosphere of plants and cause damage to their hosts; others, on the contrary, protect plants from their pathogens through direct and indirect mechanisms, thus promoting plant growth and development. These "protective" microbes are known as biocontrol agents (BCA). BCA either limit or inhibit the growth of plant pathogens, owing to the excretion of a panoply of secondary metabolites (including soluble and volatile antibiotics, siderophores, quorum sensing interfering agents). BCA can also control plant pathogens through indirect mechanisms, including competence for nutrients and space, or else by interfering with their chemical communication. That explains why some of these BCA have been included in the formulation of commercial biopesticides, which are environmentally friendly products containing live cells used to control plant diseases and pests. At present, the development of biopesticides from mesophilic microorganisms is an established technology. Unfortunately, these biopesticides are not active at low temperatures. On the other hand, the information concerning the potential use of CA-BCA for the same goal is at its infancy. Here, we review the current knowledge concerning the isolation, identification, and characterization of CA microbes which act as antagonists of plant pathogens, including the mechanisms they deploy to antagonize plant pathogens. We also illustrate their biotechnological potential to develop CA biopesticides and discuss their utility in the context of mountainous agriculture. KEY POINTS: • Many naturally occurring cold-active microbes antagonize plant pathogens. • The mechanisms of biocontrol exerted by these microbes are either direct or indirect. • Cold-active biocontrol agents can be used to develop biopesticides. • Cold-active biopesticides are crucial for sustainably intensifying agriculture in cold climates.

Insights into plant-beneficial traits of probiotic Pseudomonas chlororaphis isolates

Pseudomonas chlororaphisisolates have been studied intensively for their beneficial traits.P. chlororaphisspecies function as probiotics in plants and fish, offering plants protection against microbes, nematodes and insects. In this review, we discuss the classification ofP. chlororaphisisolates within four subspecies; the shared traits include the production of coloured antimicrobial phenazines, high sequence identity between housekeeping genes and similar cellular fatty acid composition. The direct antimicrobial, insecticidal and nematocidal effects ofP. chlororaphisisolates are correlated with known metabolites. Other metabolites prime the plants for stress tolerance and participate in microbial cell signalling events and biofilm formation among other things. Formulations ofP. chlororaphisisolates and their metabolites are currently being commercialized for agricultural use.

Microbial Ecology from the Himalayan Cryosphere Perspective

Cold-adapted microorganisms represent a large fraction of biomass on Earth because of the dominance of low-temperature environments. Extreme cold environments are mainly dependent on microbial activities because this climate restricts higher plants and animals. Himalaya is one of the most important cold environments on Earth as it shares climatic similarities with the polar regions. It includes a wide range of ecosystems, from temperate to extreme cold, distributed along the higher altitudes. These regions are characterized as stressful environments because of the heavy exposure to harmful rays, scarcity of nutrition, and freezing conditions. The microorganisms that colonize these regions are recognized as cold-tolerant (psychrotolerants) or/and cold-loving (psychrophiles) microorganisms. These microorganisms possess several structural and functional adaptations in order to perform normal life processes under the stressful low-temperature environments. Their biological activities maintain the nutrient flux in the environment and contribute to the global biogeochemical cycles. Limited culture-dependent and culture-independent studies have revealed their diversity in community structure and functional potential. Apart from the ecological importance, these microorganisms have been recognized as source of cold-active enzymes and novel bioactive compounds of industrial and biotechnological importance. Being an important part of the cryosphere, Himalaya needs to be explored at different dimensions related to the life of the inhabiting extremophiles. The present review discusses the distinct facts associated with microbial ecology from the Himalayan cryosphere perspective.

Phyllosphere Fungal Communities of Plum and Antifungal Activity of Indigenous Phenazine-Producing Pseudomonas synxantha Against Monilinia laxa

European plum (Prunus domestica L.) is a significant commercial crop in Serbia in terms of total fruit production, and is traditionally processed into slivovitz brandy. The brown rot disease caused by Monilinia laxa drastically reduces plum yield almost every year. Fungal communities associated with leaves and fruits of four local Serbian plum cultivars (Požegača, Ranka, Čačanska Lepotica and Čačanska Rodna) were investigated in two phenological stages during early (May) and late (July) fruit maturation. Alpha diversity indices showed that fungal communities were heterogeneous and Beta diversity indicated that autochthonous fungal communities depended upon seasonal changes and the cultivars themselves. The phylum Ascomycota was the most abundant in all samples, with relative abundance (RA) between 46% in the Požegača cultivar (May) and 89% in the Lepotica cultivar (July). The most abundant genus for all plum cultivars in May was Aureobasidium, with RA from 19.27 to 33.69%, followed by Cryptococcus, with 4.8 to 48.80%. In July, besides Cryptococcus, different genera (Metschnikowia, Fusarium, and Hanseniaspora) were dominant on particular cultivars. Among all cultivable fungi, molecular identification of eleven M. laxa isolates from four plum cultivars was performed simultaneously. Bacterial isolates from the plum phyllosphere were tested for their potential antifungal activity against indigenous M. laxa isolates. The most potent antagonist P4/16_1, which significantly reduced mycelial growth of M. laxa, was identified as Pseudomonas synxantha. Further characterization of P4/16_1 revealed the production of volatile organic compounds and phenazine-1-carboxylic acid (PCA). Crude benzene extract of PCA exhibited 57-63% mycelial growth inhibition of M. laxa. LC/MS analysis of the crude extract confirmed the presence of phenazine derivatives amongst other compounds. Scanning electron microscopy revealed morpho-physiological changes in the hyphae of M. laxa isolates caused by the cell culture and the P. synxantha P4/16_1 crude benzene extract. This is the first report of antagonistic activity of P. synxantha against M. laxa induced by diffusible and volatile antifungal compounds, and it appears to be a promising candidate for further investigation for potential use as a biocontrol agent against brown rot-causing fungi.

Bioprospecting cold-adapted plant growth promoting microorganisms from mountain environments

Mountain soils are challenging environments for all kinds of living things, including plants and microorganisms. Many cold-adapted microorganisms colonizing these extreme soils play important roles as promoters of plant growth and development; for that reason, they are called collectively plant growth-promoting microorganisms (PGPM). Even though there is seldom doubt concerning the usefulness of PGPM to develop eco-friendly bioinoculants, including biofertilizers and biocontrollers, a series of aspects need to be addressed in order to make this technology field-applicable. Among these aspects, the ecological and rhizosphere competences of PGPM are of paramount importance, particularly when considering the development of bioinoculants, well suited for the intensification of mountainous agricultural production. Studies on native, cold-adapted PGPM conducted in the Indian Himalayan region (IHR) and the Tropical Andes (TA) lead nowadays the research in this field. Noticeably, some common themes are emerging. For instance, soils in these mountain environments are colonized by many cold-adapted PGPM able to mobilize soil nutrients and to inhibit growth of plant pathogens. Studies aimed at deeply characterizing the abilities of such PGPM is likely to substantially contribute towards a better crop productivity in mountainous environments. The present review focuses on the importance of this microbial resource to improve crop productivity in IHR and TA. We also present a number of successful examples, which emphasize the effectiveness of some bioinoculants-developed from naturally occurring PGPM-when applied in the field.

Effects and inhibition mechanism of phenazine-1-carboxamide on the mycelial morphology and ultrastructure of Rhizoctonia solani

The purpose of this research was to explore the effect of phenazine-1-carboxamide (PCN) on Rhizoctonia solani and to elucidate its mechanisms of action. The toxicity of PCN to R. solani was measured using a growth rate method. The results indicated that PCN inhibited R. solani with a 50% effective concentration (EC₅₀) of 9.0934μg/mL. The mycelia of R. solani were then exposed to 18.18μg/mL (2EC₅₀) of PCN. Optical microscopy, scanning electron microscopy (SEM), and transmission electron microscopy (TEM) were used to observe the effects of PCN on mycelial morphology and ultrastructure. Following the PCN treatment, the optical microscopy observations revealed that the mycelia appeared twisted; the branching mycelia grew, but the main mycelia did not grow following branching; and the mycelial roots possessed more vacuoles. SEM observations revealed that the mycelia were locally swollen and exhibited a sharp decrease in prominence. TEM observations showed that the cell wall became thin and deformed; the mitochondria disappeared; the septum twisted; and most of the organelles were difficult to discern. Conversely, all of the organelles could be clearly observed in the control. We then used real-time quantitative PCR and an enzyme activity testing kit to further explore the effects of PCN on the cell wall and mitochondria. Physiological and biochemical results demonstrated that both the cell wall and mitochondria constitute are PCN targets. PCN inhibited the activities of chitin synthetase and complex I of the mitochondria electron transport chain. Molecular experiments demonstrated that PCN controlled the growth of R. solani mycelia by inhibiting the expression level of chitin synthetase genes. Future research on PCN should investigate its influence on metabolic pathways, thereby aiding in the potential development of novel pesticides.

Complete Genome Sequence of Pseudomonas Parafulva PRS09-11288, a Biocontrol Strain Produces the Antibiotic Phenazine-1-carboxylic Acid

Rhizoctonia solani is a plant pathogenic fungus, which can infect a wide range of economic crops including rice. In this case, biological control of this pathogen is one of the fundmental way to effectively control this pathogen. The Pseudomonas parafulva strain PRS09-11288 was isolated from rice rhizosphere and shows biocontrol ability against R. solani. Here, we analyzed the P. parafulva genome, which is ~ 4.7 Mb, with 4310 coding sequences, 76 tRNAs, and 7 rRNAs. Genome analysis identified a phenazine biosynthetic pathway, which can produce antibiotic phenazine-1-carboxylic acid (PCA). This compound is responsible for biocontrol ability against R. solani Kühn, which is one of the most serious fungus disease on rice. Analysis of the phenazine biosynthesis gene mutant, ΔphzF, which is very important in this pathway, confirmed the relationship between the pathway and PCA production using LC-MS profiles. The annotated full genome sequence of this strain sheds light on the role of P. parafulva PRS09-11288 as a biocontrol bacterium.

Optimisation and characterisation of the orange pigment produced by a cold adapted strain of Penicillium sp. (GBPI_P155) isolated from mountain ecosystem

With globalisation and growing health risks of synthetic colourants, search for pigments from natural sources has increased owing to their non-toxic nature. The present study highlights the bioprospection of natural pigment from a cold adapted fungal strain of Penicillium sp. (GBPI_P155), isolated from soil of Indian Himalayan region. The fungus produced insoluble and orange-coloured pigment in liquid medium with maximum production recorded in potato dextrose (PD) broth at 15°C and 3 pH, while maximum biomass was produced at 25°C and pH 3. While examining the effect of different mineral salts, and carbon and nitrogen sources on pigment production, maximum accumulation of pigment was recorded in PD broth supplemented with 2% maltose. Following production, extraction of pigment was performed using chloroform and characterised partially by UV/vis (λmax at 495 nm and a shoulder peak at 530 nm) and Fourier Transform Infrared (FT-IR) spectroscopy. Thin layer chromatography of chloroform extract resulted in separation of pigment in three fractions with Rf values 0.911, 0.852 and 0.808, which were further analysed using Liquid Chromatography Mass Spectrometry (LC/MS). The overall approach resulted in identification of pigment as a mixture of different derivatives of carotenoids. The extracted pigment also possessed antimicrobial activity against Gram-positive and Gram-negative bacteria and actinobacteria.

Biocontrol of Bacterial Leaf Blight of Rice and Profiling of Secondary Metabolites Produced by Rhizospheric Pseudomonas aeruginosa BRp3

Xanthomonas oryzae pv. oryzae (Xoo) is widely prevalent and causes Bacterial Leaf Blight (BLB) in Basmati rice grown in different areas of Pakistan. There is a need to use environmentally safe approaches to overcome the loss of grain yield in rice due to this disease. The present study aimed to develop inocula, based on native antagonistic bacteria for biocontrol of BLB and to increase the yield of Super Basmati rice variety. Out of 512 bacteria isolated from the rice rhizosphere and screened for plant growth promoting determinants, the isolate BRp3 was found to be the best as it solubilized 97 μg/ mL phosphorus, produced 30 μg/mL phytohormone indole acetic acid and 15 mg/ L siderophores in vitro. The isolate BRp3 was found to be a Pseudomonas aeruginosa based on 16S rRNA gene sequencing (accession no. HQ840693). This bacterium showed antagonism in vitro against different phytopathogens including Xoo and Fusarium spp. Strain BRp3 showed consistent pathogen suppression of different strains of BLB pathogen in rice. Mass spectrometric analysis detected the production of siderophores (1-hydroxy-phenazine, pyocyanin, and pyochellin), rhamnolipids and a series of already characterized 4-hydroxy-2-alkylquinolines (HAQs) as well as novel 2,3,4-trihydroxy-2-alkylquinolines and 1,2,3,4-tetrahydroxy-2-alkylquinolines in crude extract of BRp3. These secondary metabolites might be responsible for the profound antibacterial activity of BRp3 against Xoo pathogen. Another contributing factor toward the suppression of the pathogen was the induction of defense related enzymes in the rice plant by the inoculated strain BRp3. When used as an inoculant in a field trial, this strain enhanced the grain and straw yields by 51 and 55%, respectively, over non-inoculated control. Confocal Laser Scanning Microscopy (CLSM) used in combination with immunofluorescence marker confirmed P. aeruginosa BRp3 in the rice rhizosphere under sterilized as well as field conditions. The results provide evidence that novel secondary metabolites produced by BRp3 may contribute to its activity as a biological control agent against Xoo and its potential to promote the growth and yield of Super Basmati rice.

Prolonged Production and Aggregation Complexity of Cold-Active Lipase from Pseudomonas proteolytica (GBPI_Hb61) Isolated from Cold Desert Himalaya

Pseudomonas, being the common inhabitant of colder environments, are suitable for the production of cold-active enzymes. In the present study, a newly isolated strain of Pseudomonas from cold desert site in Indian Himalayan Region, was investigated for the production of cold-active lipase. The bacteria were identified as Pseudomonas proteolytica by 16S rDNA sequencing. Lipase production by bacteria was confirmed by qualitative assay using tributyrin and rhodamine-B agar plate method. The bacterium produced maximum lipase at 25 °C followed by production at 15 °C while utilizing olive, corn, as well as soybean oil as substrate in lipase production broth. Enzyme produced by bacteria was partially purified using ammonium sulphate fractionation. GBPI_Hb61 showed aggregation behaviour which was confirmed using several techniques including gel filtration chromatography, dynamic light scattering, and native PAGE. Molecular weight determined by SDS-PAGE followed by in-gel activity suggested two lipases of nearly similar molecular weight of ~50 kDa. The enzyme showed stability in wide range of pH from 5 to 11 and temperature up to 50 °C. The enzyme from GBPI_Hb61 exhibited maximum activity toward p-nitrophenyldecanoate (C10). The stability of enzyme was not affected with methanol while it retained more than 75% activity when incubated with ethanol, acetone, and hexane. The bacterium is likely to be a potential source for production of cold-active lipase with efficient applicability under multiple conditions.

Antagonistic Activity and Mode of Action of Phenazine-1-Carboxylic Acid, Produced by Marine Bacterium Pseudomonas aeruginosa PA31x, Against Vibrio anguillarum In vitro and in a Zebrafish In vivo Model

Phenazine and its derivatives are very important secondary metabolites produced from Pseudomonas spp. and have exhibited broad-spectrum antifungal and antibacterial activities. However, till date, there are few reports about marine derived Pseudomonas and its production of phenazine metabolites. In this study, we isolated a marine Pseudomonas aeruginosa strain PA31x which produced natural product inhibiting the growth of Vibrio anguillarum C312, one of the most serious bacterial pathogens in marine aquaculture. Combining high-resolution electro-spray-ionization mass spectroscopy and nuclear magnetic resonance spectroscopy analyses, the functional compound against V. anguillarum was demonstrated to be phenazine-1-carboxylic acid (PCA), an important phenazine derivative. Molecular studies indicated that the production of PCA by P. aeruginosa PA31x was determined by gene clusters phz1 and phz2 in its genome. Electron microscopic results showed that treatment of V. anguillarum with PCA developed complete lysis of bacterial cells with fragmented cytoplasm being released to the surrounding environment. Additional evidence indicated that reactive oxygen species generation preceded PCA-induced microbe and cancer cell death. Notably, treatment with PCA gave highly significant protective activities against the development of V. anguillarum C312 on zebrafish. Additionally, the marine derived PCA was further found to effectively inhibit the growth of agricultural pathogens, Acidovorax citrulli NP1 and Phytophthora nicotianae JM1. Taken together, this study reveals that marine Pseudomonas derived PCA carries antagonistic activities against both aquacultural and agricultural pathogens, which broadens the application fields of PCA.