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Chembiochem : a European Journal of... Jun 2020Nitrogenases catalyze the ambient reduction of N and CO at its cofactor site. Herein we present a biochemical and spectroscopic characterization of an Azotobacter...
Nitrogenases catalyze the ambient reduction of N and CO at its cofactor site. Herein we present a biochemical and spectroscopic characterization of an Azotobacter vinelandii V nitrogenase variant expressing a citrate-substituted cofactor. Designated VnfDGK , the catalytic component of this V nitrogenase variant has an αβ (δ) subunit composition and carries an 8Fe P* cluster and a citrate-substituted V cluster analogue in the αβ dimer, as well as a 4Fe cluster in the "orphaned" β-subunit. Interestingly, when normalized based on the amount of cofactor, VnfDGK shows a shift of N reduction from H evolution toward NH formation and an opposite shift of CO reduction from hydrocarbon formation toward H evolution. These observations point to a role of the organic ligand in proton delivery during catalysis and imply the use of different reaction sites/mechanisms by nitrogenase for different substrate reductions. Moreover, the increased NH /H ratio upon citrate substitution suggests the possibility to modify the organic ligand for improved ammonia synthesis in the future.
Topics: Azotobacter vinelandii; Bacterial Proteins; Citric Acid; Electron Spin Resonance Spectroscopy; Nitrogenase; Protein Conformation
PubMed: 31747483
DOI: 10.1002/cbic.201900654 -
International Journal of Molecular... Jan 2023Nitrogen-fixing bacteria execute biological nitrogen fixation through nitrogenase, converting inert dinitrogen (N) in the atmosphere into bioavailable nitrogen.... (Review)
Review
Nitrogen-fixing bacteria execute biological nitrogen fixation through nitrogenase, converting inert dinitrogen (N) in the atmosphere into bioavailable nitrogen. Elaborating the molecular mechanisms of orderly and efficient biological nitrogen fixation and applying them to agricultural production can alleviate the "nitrogen problem". is a well-established model bacterium for studying nitrogen fixation, utilizing nitrogenase encoded by the gene cluster to fix nitrogen. In , the NifA-NifL system fine-tunes the gene cluster transcription by sensing the redox signals and energy status, then modulating nitrogen fixation. In this manuscript, we investigate the transcriptional regulation mechanism of the gene in autogenous nitrogen-fixing bacteria. We discuss how autogenous nitrogen fixation can better be integrated into agriculture, providing preliminary comprehensive data for the study of autogenous nitrogen-fixing regulation.
Topics: Nitrogen Fixation; Transcription Factors; Bacterial Proteins; Nitrogenase; Azotobacter vinelandii; Genes, Bacterial; Nitrogen; Gene Expression Regulation, Bacterial
PubMed: 36674420
DOI: 10.3390/ijms24020907 -
The Science of the Total Environment Oct 2022The adverse effects of drought on plants are gradually exacerbated with global climatic change. Amelioration of the drought stress that is induced by low doses of acetic...
The adverse effects of drought on plants are gradually exacerbated with global climatic change. Amelioration of the drought stress that is induced by low doses of acetic acid (AA) has been caused great interest in plants. However, whether AA can change soil microbial composition is still unknown. Here, we investigated how exogenous AA regulates the physiology, rhizosphere soil microorganisms and metabolic composition on Salix myrtillacea under drought stress. The physiological results showed that AA could improve the drought tolerance of S. myrtillacea. Azotobacter and Pseudomonas were enriched in the rhizosphere by AA irrigation. AA significantly increased the relative contents of amino acid metabolites (e.g., glycyl-L-tyrosine, l-glutamine and seryl-tryptophan) and decreased the relative contents of phenylpropane metabolites (e.g., fraxetin and sinapyl aldehyde) in soils. The enrichments of Azotobacter and Pseudomonas were significantly correlated with glycyl-L-tyrosine, l-glutamine, seryl-tryptophan, fraxetin and sinapyl aldehyde, which could increase the stress resistance by promoting nitrogen (N) uptake for willows. Furthermore, inoculation with Azotobacter chroococcum and Pseudomonas fluorescens could significantly improve willows drought tolerance. Therefore, our results reveal that the changes of plant physiology, rhizosphere soil microorganisms and metabolic composition induced by AA can improve willows drought resistance by enhancing N uptake.
Topics: Acetic Acid; Droughts; Glutamine; Plant Roots; Plants; Rhizosphere; Salix; Soil; Soil Microbiology; Tryptophan
PubMed: 35798115
DOI: 10.1016/j.scitotenv.2022.157132 -
BMC Plant Biology Jul 2022Glycyrrhiza glabra L. is a medicinal and industrial plant that has gone extinct due to different abiotic stress caused by climate change. To understand how the...
BACKGROUND
Glycyrrhiza glabra L. is a medicinal and industrial plant that has gone extinct due to different abiotic stress caused by climate change. To understand how the plant-associated microorganism can support this plant under salinity, we collected sixteen Iranian accessions of G. glabra L., inoculated their rhizomes with Azotobacter sp. (two levels, bacterial treatments, and no-bacterial treatments, and grown them under salinity stress (NaCl levels; 0, and 200 mM).
RESULTS
Two accessions of Bardsir and Bajgah significantly showed higher resistant to salinity, for example by increasing crown diameter (11.05 and 11 cm, respectively) compared to an average diameter of 9.5 in other accessions. Azotobacter inoculation caused a significant increase in plant height and crown diameter. Among studied accessions, Kashmar (46.21%) and Ilam (44.95%) had the highest rate of membrane stability index (MSI). Evaluation of enzyme activity represented that bacterial application under salinity, increased polyphenol oxidase (PPO) (0.21 U mg protein), peroxidase (POD) (3.09 U mg protein U mg protein), and phenylalanine ammonia-lyase (PAL) (17.85 U mg protein) activity. Darab accession showed the highest increase (6.45%) in antioxidant potential compared with all studied accessions under Azotobacter inoculation. According to principal component analysis (PCA), it was found that the accession of Meshkinshahr showed a more remarkable ability to activate its enzymatic defense system under salt stress. Also, three accessions of Meshkinshahr, Eghlid, and Ilam were categorized in separated clusters than other accessions regarding various studied treatments.
CONCLUSION
Analysis indicated that five accessions of Meshkinshahr, Rabt, Piranshahr, Bardsir, and Kermanshah from the perspective of induced systematic resistance are the accessions that showed a greater morphophysiological and biochemical outcome under salinity. This study suggested that, inoculation of with Azotobacter on selected accession can relieve salt stress and support industrial mass production under abiotic condition.
Topics: Azotobacter; Endangered Species; Glycyrrhiza; Iran; Salt Stress; Triterpenes
PubMed: 35790900
DOI: 10.1186/s12870-022-03703-9 -
Journal of Basic Microbiology Mar 2023Interest in cultivating valuable medicinal plants to collect bioactive components has risen extensively over the world to meet the demands of health care systems,... (Review)
Review
Interest in cultivating valuable medicinal plants to collect bioactive components has risen extensively over the world to meet the demands of health care systems, pharmaceuticals, and food businesses. Farmers commonly use chemical fertilizers to attain maximal biomass and yield, which have negative effects on the growth, development, and bioactive constituents of such medicinally important plants. Because of its low cost, environmentally friendly behavior, and nondestructive impact on soil fertility, plant health, and human health, the use of beneficial rhizobial microbiota is an alternative strategy for increasing the production of useful medicinal plants under both standard and stressed conditions. Plant growth-promoting rhizobacteria (PGPR) associated with medicinal plants belong to the genera Azotobacter, Acinetobacter, Bacillus, Brevibacterium, Burkholderia, Exiguobacterium, Pseudomonas, Pantoea, Mycobacterium, Methylobacterium, and Serratia. These microbes enhance plant growth parameters by producing secondary metabolites, including enzymes and antibiotics, which help in nutrient uptake, enhance soil fertility, improve plant growth, and protect against plant pathogens. The role of PGPR in the production of biomass and their effect on the quality of bioactive compounds (phytochemicals) is described in this review. Additionally, the mitigation of environmental stresses including drought stress, saline stress, alkaline stress, and flooding stress to herbal plants is illustrated.
Topics: Humans; Plants, Medicinal; Plant Development; Stress, Physiological; Soil; Bacillus; Plant Roots; Soil Microbiology
PubMed: 36336634
DOI: 10.1002/jobm.202200361 -
Current Protocols Mar 2021Azotobacter vinelandii (A. vinelandii) is a commonly used model organism for the study of aerobic respiration, the bacterial production of several industrially relevant...
Azotobacter vinelandii (A. vinelandii) is a commonly used model organism for the study of aerobic respiration, the bacterial production of several industrially relevant compounds, and, perhaps most significantly, the genetics and biochemistry of biological nitrogen fixation. Laboratory growth assessments of A. vinelandii are useful for evaluating the impact of environmental and genetic modifications on physiological properties, including diazotrophy. However, researchers typically rely on manual growth methods that are oftentimes laborious and inefficient. We present a protocol for the automated growth assessment of A. vinelandii on a microplate reader, particularly well-suited for studies of diazotrophic growth. We discuss common pitfalls and strategies for protocol optimization, and demonstrate the protocol's application toward growth evaluation of strains carrying modifications to nitrogen-fixation genes. © 2021 The Authors. Basic Protocol 1: Preparation of A. vinelandii plate cultures from frozen stock Basic Protocol 2: Preparation of A. vinelandii liquid precultures Basic Protocol 3: Automated growth rate experiment of A. vinelandii on a microplate reader.
Topics: Azotobacter vinelandii; Laboratories; Nitrogen Fixation; Nitrogenase
PubMed: 33656286
DOI: 10.1002/cpz1.57 -
Environmental Science and Pollution... Mar 2023Biochar has wide application prospects as a good soil conditioner, leguminous plants can fix nitrogen and improve soil available nutrients. However, it is not clear how...
Biochar has wide application prospects as a good soil conditioner, leguminous plants can fix nitrogen and improve soil available nutrients. However, it is not clear how adding biochar when planting leguminous plants affects soil bacterial community and soil available nutrients. This study investigates the effects of biochar addition on the content of ammonia nitrogen, Olsen-P, and available potassium in northeastern farmland soils under the plantation of Trifolium repens and then compared with the application of organic fertilizer. A 90-day incubation experiment was conducted to compare the changes in the structure and relative abundance of soil microflora under varied biochar additions. It was found that the addition of biochar could affect the structure of the microflora and the available nutrients in the soil. When compared with soil planted with T. repens without the addition of biochar, with the application of 3% biochar increased the content of ammonia nitrogen, Olsen-P, and available potassium in the soil by 31.71%, 21.40%, and 11.51%, respectively. High throughput sequencing revealed that the relative abundance of functional bacteria such as azotobacter, rhizobacteria, and phosphorus solubilizing bacteria in the soil increased with the addition of biochar. Furthermore, the effect was more obvious with the addition of organic fertilizers. The addition of biochar improved the microbial community structure and increased the relative abundance of functional bacteria and the content of available nutrients in the soil. This is expected to reduce the application of chemical fertilizers, thereby protecting the environment and conserving natural resources.
Topics: Soil; Trifolium; Fertilizers; Ammonia; Charcoal; Bacteria; Nutrients; Nitrogen; Potassium; Soil Microbiology
PubMed: 36502483
DOI: 10.1007/s11356-022-24651-9 -
FEMS Microbiology Letters Nov 2022Bacteria have a mechanism to rescue stalled ribosomes known as trans-translation consisting of SsrA, a transfer-messenger RNA (tmRNA), and the small protein SmpB. Other...
Bacteria have a mechanism to rescue stalled ribosomes known as trans-translation consisting of SsrA, a transfer-messenger RNA (tmRNA), and the small protein SmpB. Other alternative rescue mechanisms mediated by ArfA and ArfB proteins are present only in some species. Ribosome rescue mechanisms also play a role in tolerance to antibiotics and various stresses such as heat. This study shows that the genome of the soil bacterium A. vinelandii harbours genes encoding for tmRNA, SmpB, two paralogs of ArfA (arfA1 and arfA2), and ArfB. A number of mutant strains carrying mutations in the ssrA, arfA1, arfA2, and arfB genes were constructed and tested for their growth and susceptibility to heat and the antibiotic tetracycline. We found that the inactivation of both ssrA and one or the two arfA genes was detrimental to growth and caused a higher susceptibility to heat and to the antibiotic tetracycline. Interestingly, the arfB mutant strain was unable to grow after 2 h of incubation at 45°C. Inactivation of arfB in the ssrA-arfA1-arfA2 strain caused a lethal phenotype since the quadruple mutant could not be isolated. Taken together, our data suggest that both arfA1 and arfA2, as well as arfB, are functional as back up mechanisms, and that the ArfB pathway has an essential role that confers A. vinelandii resistance to high temperatures.
Topics: Azotobacter vinelandii; Anti-Bacterial Agents; Hot Temperature; RNA-Binding Proteins; Ribosomes; RNA, Bacterial; Protein Biosynthesis; Tetracyclines
PubMed: 36368695
DOI: 10.1093/femsle/fnac104 -
Microorganisms Dec 2022The inoculation of plant growth-promoting bacteria (PGPB) as biofertilizers is one of the most efficient and sustainable strategies of rhizosphere manipulation leading... (Review)
Review
The inoculation of plant growth-promoting bacteria (PGPB) as biofertilizers is one of the most efficient and sustainable strategies of rhizosphere manipulation leading to increased plant biomass and yield and improved plant health, as well as the ameliorated nutritional value of fruits and edible seeds. During the last decades, exciting, but heterogeneous, results have been obtained growing PGPB inoculated plants under controlled, stressful, and open field conditions. On the other hand, the possible impact of the PGPB deliberate release on the resident microbiota has been less explored and the little available information is contradictory. This review aims at filling this gap: after a brief description of the main mechanisms used by PGPB, we focus our attention on the process of PGPB selection and formulation and we provide some information on the EU regulation for microbial inocula. Then, the concept of PGPB inocula as a tool for rhizosphere engineering is introduced and the possible impact of bacterial inoculant on native bacterial communities is discussed, focusing on those bacterial species that are included in the EU regulation and on other promising bacterial species that are not yet included in the EU regulation.
PubMed: 36557714
DOI: 10.3390/microorganisms10122462 -
Environmental Pollution (Barking, Essex... Dec 2023The use of bioretention cells as a stormwater control measure allows stormwater runoff to be collected and filtered, effectively removing microplastics and other...
The use of bioretention cells as a stormwater control measure allows stormwater runoff to be collected and filtered, effectively removing microplastics and other pollutants from stormwater. This study investigated the effect of polyethylene microplastics (PE-MPs) retention on the bioretention cell, in terms of denitrification performance and microbial community structure. Four PE-MP exposures were compared at different concentrations of 0, 250, 500 and 1000 mg/L under alternating dry and wet period conditions. Results showed that the removal efficiency reduced by 14.99%, 28.37% and 18.59% with PE-MP concentrations of 250, 500 and 1000 mg/L. The NO-N removal efficiency increased by 36.19%, 20.19% and 35.39%. After 8 days of dry conditions, the NO-N removal efficiencies of the bioretention cells were reduced by 36.66%, 46.86% and 31.11% compared to those after 2 days of dry conditions. Microbial sequencing results indicated that the accumulation of PE-MPs changed the microbial community structure within the bioretention cell filler material, promoting the growth of bacteria such as Actinobacteria, Bacteroidetes and Firmicutes. Furthermore, PE-MPs reduced the relative abundance of nitrifying bacteria (e.g. Nitrospira) within the bioretention cell and promoted denitrifying bacteria (e.g. Dechloromonas and Hydrogenophaga), along with numerous other genera such as Azotobacter and Nocardia.
Topics: Denitrification; Plastics; Polyethylene; Microplastics; Nitrogen; Rain; Bacteria
PubMed: 37778494
DOI: 10.1016/j.envpol.2023.122655