Plant Growth Promoting Rhizobacteria\u27s (PGPRS) Enzyme Dynamics in Soil Remediation

Soil is the basis of agriculture and consists of organic matters, minerals, water, and several gasses. All plants require soil both as an anchor to attach and as water and nutrient source. Unfortunately, lifestyles of humans, industrial progress, chemicals used in agriculture contaminate soil and cause soil pollution. A pollutant may be natural or human‐made in origin such as petroleum hydrocarbons, pesticides, heavy metals, and solvents. Since the quality of the soil affects the growth and product yield of plants, soil pollution is a crucial problem needs to be addressed urgently. Plant growth promoting rhizobacteria (PGPR) are microorganisms living in soil, on the plants roots, or inside the plant. PGPRs synthesize chemicals to stimulate plant growth and promote nutrient uptake, help degrading soil pollutants and fending off pathogens. While some pollutants can be degraded by enzymes produced by bacteria and fungi, degradation of heavy metals requires alternative methods. In this chapter, three enzymes produced by PGPRs are reviewed briefly. Aminocyclopropane‐1‐carboxylate (ACC) deaminase is responsible of lowering the ethylene levels of plants during stress conditions, whereas nitrogenase is responsible for N2 reduction to NH3. Moreover, phytase enables the degradation of phytate which is a main storage form of phosphate in plants

Making Soil More Accessible to Plants: The Case of Plant Growth Promoting Rhizobacteria

Plant Growth Promoting Rhizobacteria (PGPR) are beneficial soil bacteria that can live either symbiotically with plants at rhizosphere or as endophytes living on or inside of the host plants. There are two main mechanisms via PGPR contribute to the plant growth. Direct mechanism consists of phytohormone production (i.e. auxins (IAA), cytokinins and gibberellins), biological nitrogen fixation, solubilizing inorganic phosphates, mineralizing organic phosphate and producing organic matter such as amino acids. As indirect mechanisms, PGPR aid plants in combat against the pathogen microorganisms by means of stimulating the disease-resistance mechanism of plants, promote favorable symbiosis, decontaminate the soil of xenobiotics. PGPR can also help plants to cope against abiotic stress by lowering ethylene levels, or against pathogenic microorganism by means of secreting antibacterial/antifungal substances. Exact mechanisms of PGPR characteristics which stimulate the plant growth or product formation are still under investigation, yet in agriculture, PGPR are used as environmental friendly biofertilizers, biocontrol agents or biostimulants. These beneficial bacteria are usually introduced to the plants either in powder or liquid form or the seeds are covered with the inoculants before sowing. Plants are subject to many different environmental elements. Abiotic factors such as drought or water stress have been one of the main plant growth limiting factors. Agricultural PGPR application is an alternative solution against loss due to the environmental stresses, since breeding a plant with stress resistance trait is a very long and tricky process due to the fact that such traits are controlled by multiple genes. PGPR phytohormone and enzyme (i.e. ACC deaminase) production can decrease the stress levels of plants while enhancing the root structures

Isolation and characterization of natural protease producers of Bacillus spp. from Soil samples

Proteases are group of enzymes that catalyze the hydrolysis of proteins, resulting in peptide and amino acid production. These are considered as commercially most significant among industrial enzymes, consisting about 60% of the total enzyme market. Proteases have wide areas of application in several industries like food, detergent, textile, pulp and paper, and pharmaceutical industries, as these offer environmentally benign, sustainable solutions to several challenges in the corresponding industry.Enzymes can be produced by plants, animals or microorganisms, yet the majority is produced by (recombinant) microorganisms, typically with modified features for high enzyme production. However, for e.g. food industry, the use of genetically modified microorganisms is not preferred, therefore isolation of wild-type microorganism strains for enzyme production is a necessary and valuable process. Here we present the results of screening, isolation and characterization of new Bacillus spp. for protease production from soil samples from different areas in Kosovo. Soil samples were divided into four different groups according to their origin: (i) isolates from areas polluted by heavy industry, (ii) isolates from high altitude, (iii) loess sample near thermal water springs, and (iv) workable area land. Soil samples were extracted by sterile saline solution, the extract was screened for protease production by using 1% skim milk agar. Best strains were identified as protease production by clear zone formed around colonies, selected colonies were used for further investigation

Enzyme Dynamic in Plant Nutrition Uptake and Plant Nutrition

Soil contains enzymes, constantly interacting with soil constituents, e.g. minerals, rhizosphere and numerous nutrients. Enzymes, in turn, catalyse important biochemical reactions for rhizobacteria and plants, stabilize the soil by degrading wastes and mediate nutrient recycling.The available enzymes inside soil could originate from plants, animals or microbes. The enzymes that are produced from these organism could exhibit intracellular activities, at the cell membrane, interacting therefore with soil and its constituents, or extracellularly (so freely available). Therefore, vis-à-vis to plant nutrition, the (extra or sub) cellular localization has a key role. Typical major enzymes available in soil can be listed as dehydrogenases, hydrogenases, oxidases, catalases, peroxidases, phenol o-hydroxylase, dextransucrase, aminotransferase, rhodanese, carboxylesterase, lipase, phosphatase, nuclease, phytase, arylsulphatase, amylase, cellulase, inulase, xylanase, dextranase, levanase, poly-galacturonase, glucosidase, galactosidase, invertase, peptidase, asparaginase, glutaminase, amidase, urease, aspartate decarboxylase, glutamate decarboxylase and aromatic amino acid decarboxylase. An interesting strategy for improving the nutritional quality of the soil would be to inoculate microorganism to soil while giving attention to mineral or other compounds that affect enzyme activity in soil. Since, some elements or compounds could show both activation and inhibitory effect, such as Fe, Na, etc. metals, the regulation of their bioavailability is crucial

The Role of Soil Beneficial Bacteria in Wheat Production: A Review

Free-living plant growth-promoting rhizobacteria (PGPR) have favourable effect on plant growth, tolerance against stresses and are considered as a promising alternative to inorganic fertilizer for promoting plant growth, yield and quality. PGPR colonize at the plant root, increase germination rates, promote root growth, yield, leaf area, chlorophyll content, nitrogen content, protein content, tolerance to drought, shoot and root weight, and delayed leaf senescence. Several important bacterial characteristics, such as biological nitrogen fixation, solubilization of inorganic phosphate and mineralization of organic phosphate, nutrient uptake, 1-aminocydopropane-1-carboxylic acid (ACC) deaminase activity and production of siderophores and phytohormones, can be assessed as plant growth promotion traits. By efficient use, PGPR is expected to contribute to agronomic efficiency, chiefly by decreasing costs and environmental pollution, by eliminating harmful chemicals. This review discusses various bacteria acting as PGPR, their genetic diversity, screening strategies, working principles, applications for wheat and future aspects in terms of efficiency, mechanisms and the desirable properties. The elucidation of the diverse mechanisms will enable microorganisms developing agriculture further

A method for estimation of elasticities in metabolic networks using steady state and dynamic metabolomics data and linlog kinetics

BACKGROUND: Dynamic modeling of metabolic reaction networks under in vivo conditions is a crucial step in order to obtain a better understanding of the (dis)functioning of living cells. So far dynamic metabolic models generally have been based on mechanistic rate equations which often contain so many parameters that their identifiability from experimental data forms a serious problem. Recently, approximative rate equations, based on the linear logarithmic (linlog) format have been proposed as a suitable alternative with fewer parameters. RESULTS: In this paper we present a method for estimation of the kinetic model parameters, which are equal to the elasticities defined in Metabolic Control Analysis, from metabolite data obtained from dynamic as well as steady state perturbations, using the linlog kinetic format. Additionally, we address the question of parameter identifiability from dynamic perturbation data in the presence of noise. The method is illustrated using metabolite data generated with a dynamic model of the glycolytic pathway of Saccharomyces cerevisiae based on mechanistic rate equations. Elasticities are estimated from the generated data, which define the complete linlog kinetic model of the glycolysis. The effect of data noise on the accuracy of the estimated elasticities is presented. Finally, identifiable subset of parameters is determined using information on the standard deviations of the estimated elasticities through Monte Carlo (MC) simulations. CONCLUSION: The parameter estimation within the linlog kinetic framework as presented here allows the determination of the elasticities directly from experimental data from typical dynamic and/or steady state experiments. These elasticities allow the reconstruction of the full kinetic model of Saccharomyces cerevisiae, and the determination of the control coefficients. MC simulations revealed that certain elasticities are potentially unidentifiable from dynamic data only. Addition of steady state perturbation of enzyme activities solved this problem