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Molecular Plant-microbe Interactions :... Sep 2023spp. make up 1.6% of the bacteria in the soil and are found throughout the world. More than 140 species of this genus have been identified, some beneficial to the...
spp. make up 1.6% of the bacteria in the soil and are found throughout the world. More than 140 species of this genus have been identified, some beneficial to the plant. Several species in the family Pseudomonadaceae, including AvOP, A1501, DSM4166, 6HT33bT, and sp. strain K1 can fix nitrogen from the air. The genes required for these reactions are organized in a nitrogen fixation island, obtained via horizontal gene transfer from , , and . Today, this island is conserved in spp. from different geographical locations, which, in turn, have evolved to deal with different geo-climatic conditions. Here, we summarize the molecular mechanisms behind -driven plant growth promotion, with particular focus on improving plant performance at limiting nitrogen (N) and improving plant N content. We describe -plant interaction strategies in the soil, noting that the mechanisms of denitrification, ammonification, and secondary metabolite signaling are only marginally explored. Plant growth promotion is dependent on the abiotic conditions and differs at sufficient and deficient N. The molecular controls behind different plant responses are not fully elucidated. We suggest that superposition of transcriptome, proteome, and metabolome data and their integration with plant phenotype development through time will help fill these gaps. The aim of this review is to summarize the knowledge behind -driven nitrogen fixation and to point to possible agricultural solutions. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
PubMed: 36989040
DOI: 10.1094/MPMI-10-22-0223-CR -
Biophysical Chemistry Oct 2021The MoFe protein component of the nitrogenase enzyme complex is the substrate reducing site and contains two sets of symmetrically arrayed metallo centers called the P...
The MoFe protein component of the nitrogenase enzyme complex is the substrate reducing site and contains two sets of symmetrically arrayed metallo centers called the P (FeS) and the FeMoco (MoFeS-C-homocitrate) centers. The ATP-binding Fe protein is the specific reductant for the MoFe protein. Both symmetrical halves of the MoFe protein are thought to function independently during nitrogenase catalysis. Forming [AlF] transition-state complexes between the MoFe protein and the Fe protein of Azotobacter vinelandii ranging from 0 to 2 Fe protein/MoFe protein produced a series of complexes whose specific activity decreases with increase in bound Fe protein/MoFe protein ratio. Reduction of 2H to H was inhibited in a linear manner with an x-intercept at 2.0 with increasing Fe protein binding, whereas acetylene reduction to ethylene decreased more rapidly with an x-intercept near 1.5. H reduction is a distinct process occurring independently at each half of the MoFe protein but acetylene reduction decreases more rapidly than H reduction with increasing Fe protein/MoFe protein ratio, suggesting that a response is transmitted between the two αβ halves of the MoFe protein for acetylene reduction as Fe protein is bound. A mechanistic model is derived to investigate this behavior. The model predicts that each site functions independently for 2H reduction to H. For acetylene reduction, the model predicts positive (synchronous) not negative cooperativity arising from acetylene binding to both sites before substrate reduction occurs. When this model is applied to inhibition by Cp2 and modified Av2 protein (L127∆) that form strong, non-dissociable complexes, positive cooperativity is absent and each site acts independently. The results suggest a new paradigm for the catalytic function of the MoFe protein during nitrogenase catalysis.
Topics: Acetylene; Azotobacter vinelandii; Nitrogenase
PubMed: 34242995
DOI: 10.1016/j.bpc.2021.106650 -
Frontiers in Bioengineering and... 2020Poly-(3-hydroxyalkanoates) (PHAs) are bacterial carbon and energy storage compounds. These polymers are synthesized under conditions of nutritional imbalance, where a... (Review)
Review
Poly-(3-hydroxyalkanoates) (PHAs) are bacterial carbon and energy storage compounds. These polymers are synthesized under conditions of nutritional imbalance, where a nutrient is growth-limiting while there is still enough carbon source in the medium. On the other side, the accumulated polymer is mobilized under conditions of nutrient accessibility or by limitation of the carbon source. Thus, it is well known that the accumulation of PHAs is affected by the availability of nutritional resources and this knowledge has been used to establish culture conditions favoring high productivities. In addition to this effect of the metabolic status on PHAs accumulation, several genetic regulatory networks have been shown to drive PHAs metabolism, so the expression of the PHAs genes is under the influence of global or specific regulators. These regulators are thought to coordinate PHAs synthesis and mobilization with the rest of bacterial physiology. While the metabolic and biochemical knowledge related to the biosynthesis of these polymers has led to the development of processes in bioreactors for high-level production and also to the establishment of strategies for metabolic engineering for the synthesis of modified biopolymers, the use of knowledge related to the regulatory circuits controlling PHAs metabolism for strain improvement is scarce. A better understanding of the genetic control systems involved could serve as the foundation for new strategies for strain modification in order to increase PHAs production or to adjust the chemical structure of these biopolymers. In this review, the regulatory systems involved in the control of PHAs metabolism are examined, with emphasis on those acting at the level of expression of the enzymes involved and their potential modification for strain improvement, both for higher titers, or manipulation of polymer properties. The case of the PHAs producer is taken as an example of the complexity and variety of systems controlling the accumulation of these interesting polymers in response to diverse situations, many of which could be engineered to improve PHAs production.
PubMed: 32426348
DOI: 10.3389/fbioe.2020.00386 -
Scientific Reports Apr 2023Free-living bacterial community and abundance have been investigated extensively under different soil management practices. However, little is known about their nitrogen...
Free-living bacterial community and abundance have been investigated extensively under different soil management practices. However, little is known about their nitrogen (N) fixation abilities, and how their contributions to N budgets impact plant growth, yield, and carbon (C) and N cycling enzymes in a long-term consecutive sugarcane monoculture farming system, under contrasting amendments, along different soil horizons. Here, nifH gene amplicon was used to investigate diazotrophs bacterial community and abundance by leveraging high-throughput sequencing (HTS). Moreover, edaphic factors in three soil depths (0-20, 20-40, and 40-60 cm) under control (CK), organic matter (OM), biochar (BC), and filter mud (FM) amended soils were investigated. Our analysis revealed that β-glucosidase activity, acid phosphatase activity, ammonium (NH-N), nitrate (NON), total carbon (TC), total nitrogen (TN), and available potassium (AK) were considerably high in 0-20 cm in all the treatments. We also detected a significantly high proportion of Proteobacteria and Geobacter in the entire sample, including Anabaena and Enterobacter in 0-20 cm soil depth under the BC and FM amended soils, which we believed were worthy of promoting edaphic factors and sugarcane traits. This phenomenon was further reinforced by network analysis, where diazotrophs bacteria belonging to Proteobacteria exhibited strong and positive associations soil electrical conductivity (EC), soil organic matter content (SOM) available phosphorus (AP), TN, followed by NH4-N and NON, a pattern that was further validated by Mantel test and Pearson's correlation coefficients analyses. Furthermore, some potential N-fixing bacteria, including Burkholderia, Azotobacter, Anabaena, and Enterobacter exhibited a strong and positive association with sugarcane agronomic traits, namely, sugarcane stalk, ratoon weight, and chlorophyll content. Taken together, our findings are likely to broaden our understanding of free-living bacteria N-fixation abilities, and how their contributions to key soil nutrients such as N budgets impact plant growth and yield, including C and N cycling enzymes in a long-term consecutive sugarcane monoculture farming system, under contrasting amendments, along different soil horizons.
Topics: Soil; Saccharum; Bacteria; Carbon; Proteobacteria; Nitrogen; Fertilization; Soil Microbiology
PubMed: 37072423
DOI: 10.1038/s41598-022-25807-w -
Plants (Basel, Switzerland) Aug 2023The problem of phosphorus and nitrogen deficiency in agricultural soils has been solved by adding chemical fertilizers. However, their excessive use and their...
The problem of phosphorus and nitrogen deficiency in agricultural soils has been solved by adding chemical fertilizers. However, their excessive use and their accumulation have only contributed to environmental contamination. Given the high content of nutrients in biosolids collected from a food industry waste treatment plant, their use as fertilizers was investigated in plants grown in sandy loam soil collected from a semi-desert area. These biosolids contained insoluble phosphorus sources; therefore, given the ability of to solubilize phosphates, this strain was incorporated into the study. In vitro, the suitable conditions for the growth of plants were determined by using biosolids as a fertilizer and as a plant-growth-promoting microorganism; in vitro, the ability of to solubilize phosphates, fix nitrogen, and produce indole acetic acid, a phytohormone that promotes root formation, was also evaluated. At the greenhouse stage, the plants fertilized with biosolids at concentrations of 15 and 20% (/) and inoculated with favored the development of bending strength plants, which was observed on the increased stem diameter (>13.5% compared with the negative control and >7.4% compared with the positive control), as well as a better absorption of phosphorus and nitrogen, the concentration of which increased up to 62.8% when compared with that in the control treatments. The interactions between plants and were observed via scanning electron microscopy. The application of biosolids and in plants grown in greenhouses presented better development than when plants were treated with a chemical fertilizer. The enhanced plant growth was attributed to the increase in root surface area.
PubMed: 37687299
DOI: 10.3390/plants12173052 -
Applied and Environmental Microbiology Sep 2022Biological nitrogen fixation requires large amounts of energy in the form of ATP and low potential electrons to overcome the high activation barrier for cleavage of the...
Biological nitrogen fixation requires large amounts of energy in the form of ATP and low potential electrons to overcome the high activation barrier for cleavage of the dinitrogen triple bond. The model aerobic nitrogen-fixing bacteria, Azotobacter vinelandii, generates low potential electrons in the form of reduced ferredoxin (Fd) and flavodoxin (Fld) using two distinct mechanisms via the enzyme complexes Rnf and Fix. Both Rnf and Fix are expressed during nitrogen fixation, but deleting either or genes has little effect on diazotrophic growth. However, deleting both and eliminates the ability to grow diazotrophically. Rnf and Fix both use NADH as a source of electrons, but overcoming the energetics of NADH's endergonic reduction of Fd/Fld is accomplished through different mechanisms. Rnf harnesses free energy from the chemiosmotic potential, whereas Fix uses electron bifurcation to effectively couple the endergonic reduction of Fd/Fld to the exergonic reduction of quinone. Different reaction stoichiometries and condition-specific differential gene expression indicate specific roles for the two reactions. This work's complementary physiological studies and thermodynamic modeling reveal how Rnf and Fix balance redox homeostasis in various conditions. Specifically, the Fix complex is required for efficient growth under low oxygen concentrations, while Rnf is presumed to maintain reduced Fd/Fld production for nitrogenase under standard conditions. This work provides a framework for understanding how the production of low potential electrons sustains robust nitrogen fixation in various conditions. The availability of fixed nitrogen is critical for life in many ecosystems, from extreme environments to agriculture. Due to the energy demands of biological nitrogen fixation, organisms must tailor their metabolism during diazotrophic growth to deliver the energy requirements to nitrogenase in the form of ATP and low potential electrons. Therefore, a complete understanding of diazotrophic energy metabolism and redox homeostasis is required to understand the impact on ecological communities or to promote crop growth in agriculture through engineered diazotrophs.
Topics: Adenosine Triphosphate; Azotobacter vinelandii; Ecosystem; Ferredoxins; NAD; Nitrogen; Nitrogen Fixation; Nitrogenase
PubMed: 36000884
DOI: 10.1128/aem.01049-22 -
Journal of Fungi (Basel, Switzerland) Apr 2022Antifungal efficacy of against trichothecene-producing spp. was investigated in maize, sorghum, and wheat. The three cereals were subjected to four treatments as...
Antifungal efficacy of against trichothecene-producing spp. was investigated in maize, sorghum, and wheat. The three cereals were subjected to four treatments as control (T1), alone (T2), combination of and treatment (T3), and only (T4). All the treatments were evaluated for total mass of seedlings, root and shoot length, seed germination, and vigor index (VI), and extent of rhizoplane colonization by was investigated. Further, greenhouse studies were conducted to learn the efficacy of in vivo conditions. Antifungal efficacy was tested by the dual-culture method which resulted in significant reduction in growth. Infection by was reduced up to 50% in treated cereals such as maize, sorghum, and wheat, and there was also significant increase in seedling mass in the three hosts. Maize showed the highest VI (1859.715), followed by sorghum (1470.84), and wheat (2804.123) with treatment. In addition, seed germination was enhanced to 76% in maize, 69% in sorghum, and 68% in wheat, respectively. Efficacy of rhizoplane colonization showed successful isolation of with high CFU rate, and furthermore, significant colonization inhibition by spp. was observed. In the greenhouse conditions, on the 45th day of the experimental set-up, the highest shoot length/root length recorded in maize was 155.70/70.0 cm, in sorghum 165.90/48.0 cm, and in wheat 77.85/56.0 cm, and the maximum root mass recorded was 17.53 g in maize, 4.52 g in sorghum, and 1.90 g in wheat. Our present study showed that seed treatment by may be used as an alternate biocontrol method against infection in maize, sorghum, and wheat.
PubMed: 35628729
DOI: 10.3390/jof8050473 -
International Journal of Biological... Aug 2023This study involved the extraction of an exopolysaccharide (EPS) from Azotobacter salinestris AZ-6, which was isolated from soil cultivated with leguminous plants. In a...
This study involved the extraction of an exopolysaccharide (EPS) from Azotobacter salinestris AZ-6, which was isolated from soil cultivated with leguminous plants. In a medium devoid of nitrogen, the AZ-6 strain displayed a maximum EPS yield of 1.1 g/l and the highest relative viscosity value of 3.4. The homogeneity of the polymer was demonstrated by the average molecular weight of 1.61 × 10 Da and a retention time of 17.211 min for levan. The presence of characteristic functional groups and structural units of carbohydrate polymers has been confirmed through spectroscopic analyses utilizing Fourier-transform infrared (FT-IR) and nuclear magnetic resonance (NMR) techniques. Thermogravimetric analysis (TGA) revealed a noteworthy decrease in weight (74 %) in the temperature range spanning from 260 to 350 °C. X-ray diffraction (XRD) was utilized to verify the crystalline and amorphous characteristics of EPS-AZ-6. The EPS-AZ-6 exhibited significant cytotoxicity against the MCF-7 tumor cell line, as evidenced by an IC value of 6.39 ± 0.05 μg/ml. It also demonstrated a moderate degree of cytotoxicity towards HepG-2 cell line, as indicated by an IC value of 29.79 ± 0.41 μg/ml. EPS-AZ-6 exhibited potent antioxidant and in vitro antibacterial properties. These characteristics suggest the potential application value of EPS-AZ-6 in the food industry and pharmaceutical applications.
Topics: Spectroscopy, Fourier Transform Infrared; Azotobacter; Antioxidants; Molecular Weight; Polysaccharides, Bacterial
PubMed: 37390994
DOI: 10.1016/j.ijbiomac.2023.125594 -
PeerJ 2021Organic and biological fertilizers are considered as a very important source of plant nutrients. A field experiment was conducted during 2017-2018 in paddy soil to...
Organic and biological fertilizers are considered as a very important source of plant nutrients. A field experiment was conducted during 2017-2018 in paddy soil to investigate the effect of vermicomposting of cattle manure mixture with and rice straw on soil microbial activity, nutrient uptake, and grain yield under inoculation of N-fixing bacteria. Experimental factors consisted of organic amendments at six levels (vermicomposts prepared from manure (VM); manure + rice straw (VRM); manure + mixture (VAM); manure + rice straw + mixture (VRAM); raw manure without vermicomposting (M), and a control) and N-fixing bacteria at three levels (, , and non-inoculation). The results showed that, vermicompost treatments compared to control and raw manure significantly increased the number and biomass-C of soil microorganisms, urease activity, number of tillers hill, phosphorus (P) and potassium (K) uptake, and grain and protein yield. Inoculation of plants with N-fixing bacteria, especially increased the efficiency of organic amendments, so that the maximum urease activity, soil microbial activity, P and N uptake, and grain yield (4,667 (2017) and 5,081 (2018) kg/h) were observed in vermicompost treatments containing (VAM and VRAM) under inoculation with . The results of the study suggested that, using an organic source along with inoculation with appropriate N-fixing bacteria for vermicompost has a great effect on enzyme activity, soil biology, nutrient uptake and grain yield has a synergistic interaction on agronomic traits under flooded conditions. Therefore, this nutrient method can be used as one of the nutrient management strategies in the sustainable rice production.
PubMed: 34557340
DOI: 10.7717/peerj.10833 -
Applied Microbiology and Biotechnology Sep 2023Reductive soil disinfestation (RSD) is an effective bioremediation technique to restructure the soil microbial community and eliminate soilborne phytopathogens. Yet we...
Reductive soil disinfestation (RSD) is an effective bioremediation technique to restructure the soil microbial community and eliminate soilborne phytopathogens. Yet we still lack a comprehensive understanding of the keystone taxa involved and their roles in ecosystem functioning in degraded soils treated by RSD. In this study, the bacteriome network structure in RSD-treated soil and the subsequent cultivation process were explored. As a result, bacterial communities in RSD-treated soil developed more complex topologies and stable co-occurrence patterns. The richness and diversity of keystone taxa were higher in the RSD group (module hub: 0.57%; connector: 23.98%) than in the Control group (module hub: 0.16%; connector: 19.34%). The restoration of keystone taxa in RSD-treated soil was significantly (P < 0.01) correlated with soil pH, total organic carbon, and total nitrogen. Moreover, a strong negative correlation (r = -0.712; P < 0.01) was found between keystone taxa richness and Fusarium abundance. Our results suggest that keystone taxa involved in the RSD network structure are capable of maintaining a flexible generalist mode of metabolism, namely with respect to nitrogen fixation, methylotrophy, and methanotrophy. Furthermore, distinct network modules composed by numerous anti-pathogen agents were formed in RSD-treated soil; i.e., the genera Hydrogenispora, Azotobacter, Sphingomonas, and Clostridium_8 under the soil treatment stage, and the genera Anaerolinea and Pseudarthrobacter under the plant cultivation stage. The study provides novel insights into the association between fungistasis and keystone or sensitive taxa in RSD-treated soil, with significant implications for comprehending the mechanisms of RSD. KEY POINTS: • RSD enhanced bacteriome network stability and restored keystone taxa. • Keystone taxa richness was negatively correlated with Fusarium abundance. • Distinct sensitive OTUs and modules were formed in RSD soil.
Topics: Soil; Bacteria; Microbiota; Fusarium; Firmicutes; Soil Microbiology
PubMed: 37450017
DOI: 10.1007/s00253-023-12676-0