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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 -
Microbial Genomics Sep 2022There is an urgent need to replace petroleum-based plastic with bio-based and biodegradable alternatives. Polyhydroxyalkanoates (PHAs) are attractive prospective...
There is an urgent need to replace petroleum-based plastic with bio-based and biodegradable alternatives. Polyhydroxyalkanoates (PHAs) are attractive prospective replacements that exhibit desirable mechanical properties and are recyclable and biodegradable in terrestrial and marine environments. However, the production costs today still limit the economic sustainability of the PHA industry. Seaweed cultivation represents an opportunity for carbon capture, while also supplying a sustainable photosynthetic feedstock for PHA production. We mined existing gene and protein databases to identify bacteria able to grow and produce PHAs using seaweed-derived carbohydrates as substrates. There were no significant relationships between the genes involved in the deconstruction of algae polysaccharides and PHA production, with poor to negative correlations and diffused clustering suggesting evolutionary compartmentalism. We identified 2 987 bacterial candidates spanning 40 taxonomic families predominantly within Alphaproteobacteria, Gammaproteobacteria and Burkholderiales with enriched seaweed-degrading capacity that also harbour PHA synthesis potential. These included highly promising candidates with specialist and generalist specificities, including , , , , , , , , , , , , , , , , , , , , and . In this enriched subset, the family-level densities of genes targeting green macroalgae polysaccharides were considerably higher (=231.6±68.5) than enzymes targeting brown (=65.34±13.12) and red (=30.5±10.72) polysaccharides. Within these organisms, an abundance of genes was observed, suggesting that the fatty acid synthesis pathway supplies (R)-3-hydroxyacyl-CoA or 3-hydroxybutyryl-CoA from core metabolic processes and is the predominant mechanism of PHA production in these organisms. Our results facilitate extending seaweed biomass valorization in the context of consolidated biorefining for the production of bioplastics.
Topics: Bacteria; Carbohydrates; Carbon; Coenzyme A; Fatty Acids; Humans; Petroleum; Plastics; Polyhydroxyalkanoates; Prospective Studies; Seaweed
PubMed: 36125959
DOI: 10.1099/mgen.0.000866 -
Journal of Experimental Botany Jul 2020Nitrogen (N) is an essential element for plant productivity, thus, it is abundantly applied to the soil in the form of organic or chemical fertilizers that have negative... (Review)
Review
Nitrogen (N) is an essential element for plant productivity, thus, it is abundantly applied to the soil in the form of organic or chemical fertilizers that have negative impacts on the environment. Exploiting the potential of beneficial microbes and identifying crop genotypes that can capitalize on symbiotic associations may be possible ways to significantly reduce the use of N fertilizers. The best-known example of symbiotic association that can reduce the use of N fertilizers is the N2-fixing rhizobial bacteria and legumes. Bacterial taxa other than rhizobial species can develop associative symbiotic interactions with plants and also fix N. These include bacteria of the genera Azospirillum, Azotobacter, and Bacillus, some of which are commercialized as bio-inoculants. Arbuscular mycorrhizal fungi are other microorganisms that can develop symbiotic associations with most terrestrial plants, favoring access to nutrients in a larger soil volume through their extraradical mycelium. Using combinations of different beneficial microbial species is a promising strategy to boost plant N acquisition and foster a synergistic beneficial effect between symbiotic microorganisms. Complex biological mechanisms including molecular, metabolic, and physiological processes dictate the establishment and efficiency of such multipartite symbiotic associations. In this review, we present an overview of the current knowledge and future prospects regarding plant N nutrition improvement through the use of beneficial bacteria and fungi associated with plants, individually or in combination.
Topics: Bacteria; Fungi; Mycorrhizae; Nitrogen; Plant Roots; Soil; Soil Microbiology; Symbiosis
PubMed: 32157312
DOI: 10.1093/jxb/eraa112 -
Biochemistry Feb 2018Photoinduced charge-transfer dynamics and the influence of cluster size on the dynamics were investigated using five iron-sulfur clusters: the 1Fe-4S cluster in...
Photoinduced charge-transfer dynamics and the influence of cluster size on the dynamics were investigated using five iron-sulfur clusters: the 1Fe-4S cluster in Pyrococcus furiosus rubredoxin, the 2Fe-2S cluster in Pseudomonas putida putidaredoxin, the 4Fe-4S cluster in nitrogenase iron protein, and the 8Fe-7S P-cluster and the 7Fe-9S-1Mo FeMo cofactor in nitrogenase MoFe protein. Laser excitation promotes the iron-sulfur clusters to excited electronic states that relax to lower states. The electronic relaxation lifetimes of the 1Fe-4S, 8Fe-7S, and 7Fe-9S-1Mo clusters are on the picosecond time scale, although the dynamics of the MoFe protein is a mixture of the dynamics of the latter two clusters. The lifetimes of the 2Fe-2S and 4Fe-4S clusters, however, extend to several nanoseconds. A competition between reorganization energies and the density of electronic states (thus electronic coupling between states) mediates the charge-transfer lifetimes, with the 2Fe-2S cluster of Pdx and the 4Fe-4S cluster of Fe protein lying at the optimum leading to them having significantly longer lifetimes. Their long lifetimes make them the optimal candidates for long-range electron transfer and as external photosensitizers for other photoactivated chemical reactions like solar hydrogen production. Potential electron-transfer and hole-transfer pathways that possibly facilitate these charge transfers are proposed.
Topics: Azotobacter vinelandii; Bacteria; Bacterial Proteins; Catalytic Domain; Electron Transport; Ferredoxins; Iron-Sulfur Proteins; Models, Molecular; Oxidation-Reduction; Oxidoreductases; Protein Conformation; Pseudomonas putida; Pyrococcus furiosus; Rubredoxins
PubMed: 29303562
DOI: 10.1021/acs.biochem.7b01159 -
Frontiers in Microbiology 2021Diazotrophs that carry out the biological fixation of atmospheric dinitrogen (N) replenish biologically available nitrogen (N) in soil and are influenced by the input of...
Diazotrophs that carry out the biological fixation of atmospheric dinitrogen (N) replenish biologically available nitrogen (N) in soil and are influenced by the input of inorganic and organic substrates. To date, little is known about the effects of combined organic substrate addition and N fertilization on the diazotroph community composition and structure in purple soils. We investigated the effects of N fertilization and straw mulching on diazotroph communities by quantifying and sequencing the gene in wheat rhizosphere. The abundance and richness of diazotrophs were greater the higher the fertilization level in the mulched treatments, whereas in the nonmulched treatments (NSMs), richness was lowest with the highest N fertilization level. The abundance and α-diversity of diazotrophs correlated with most of the soil properties but not with pH. At the genus level, the relative abundances of , , and were higher in the NSMs and those of , , , , , , , and in the mulched treatments. The differences in community composition between the mulched and the NSMs were associated with differences in soil temperature and soil organic carbon and available potassium contents and C:N ratio. Overall, straw mulching and N fertilization were associated with changes in diazotroph community composition and higher abundance of gene in alkaline purple soils.
PubMed: 34093473
DOI: 10.3389/fmicb.2021.658668 -
Scientific Reports Sep 2022Licorice (Glycyrrhiza glabra L.) is an industrial medicinal plant that is potentially threatened by extinction. In this study, the effects of salinity (0 and 200 mM...
Licorice (Glycyrrhiza glabra L.) is an industrial medicinal plant that is potentially threatened by extinction. In this study, the effects of salinity (0 and 200 mM sodium chloride (NaCl)) and Azotobacter inoculation were evaluated on 16 licorice accessions. The results showed that salinity significantly reduced the fresh and dry biomass (FW and DW, respectively) of roots, compared to plants of the control group (a decrease of 15.92% and 17.26%, respectively). As a result of bacterial inoculation, the total sugar content of roots increased by 21.56% when salinity was applied, but increased by 14.01% without salinity. Salinity stress increased the content of glycyrrhizic acid (GA), phenols, and flavonoids in licorice roots by 104.6%, 117.2%, and 56.3%, respectively. Integrated bacterial inoculation and salt stress significantly increased the GA content in the accessions. Bajgah and Sepidan accessions had the highest GA contents (96.26 and 83.17 mg/g DW, respectively), while Eghlid accession had the lowest (41.98 mg/g DW). With the bacterial application, the maximum amounts of glabridin were obtained in Kashmar and Kermanshah accessions (2.04 and 1.98 mg/g DW, respectively). Bajgah and Kashmar accessions had higher amounts of rutin in their aerial parts (6.11 and 9.48 mg/g DW, respectively) when their roots were uninoculated. In conclusion, these results can assist in selecting promising licorice accessions for cultivation in harsh environments.
Topics: Azotobacter; Flavonoids; Glycyrrhiza; Glycyrrhizic Acid; Iran; Phenols; Plant Extracts; Plant Roots; Rutin; Salinity; Salt Stress; Sodium Chloride; Sugars; Triterpenes
PubMed: 36151202
DOI: 10.1038/s41598-022-20366-6 -
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 -
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 -
Polish Journal of Microbiology Aug 2016The excessive use of mineral fertilizers causes many negative consequences for the environment as well as potentially dangerous effects of chemical residues in plant... (Review)
Review
The excessive use of mineral fertilizers causes many negative consequences for the environment as well as potentially dangerous effects of chemical residues in plant tissues on the health of human and animal consumers. Bio-fertilizers are formulations of beneficial microorganisms, which upon application can increase the availability of nutrients by their biological activity and help to improve soil health. Microbes involved in the formulation of bio-fertilizers not only mobilize N and P but mediate the process of producing crops and foods naturally. This method avoids the use of synthetic chemical fertilizers and genetically modified organisms to influence the growth of crops. In addition to their role in enhancing the growth of the plants, biofertilizers can act as biocontrol agents in the rhizosphere at the same time. Biofertilizers are very safe for human, animal and environment. The use of Azotobacter, Azospirillum, Pseudomonas, Acetobacter, Burkholderia, Bacillus, Paenibacillus and some members of the Enterobacteriaceae is gaining worldwide importance and acceptance and appears to be the trend for the future.
Topics: Agricultural Inoculants; Agriculture; Fertilizers; Malus; Plant Diseases; Soil Microbiology
PubMed: 29334068
DOI: 10.5604/17331331.1215599 -
Frontiers in Microbiology 2018Flavin-based electron bifurcation is a newly discovered mechanism, by which a hydride electron pair from NAD(P)H, coenzyme FH, H, or formate is split by flavoproteins... (Review)
Review
Flavin-based electron bifurcation is a newly discovered mechanism, by which a hydride electron pair from NAD(P)H, coenzyme FH, H, or formate is split by flavoproteins into one-electron with a more negative reduction potential and one with a more positive reduction potential than that of the electron pair. Via this mechanism microorganisms generate low- potential electrons for the reduction of ferredoxins (Fd) and flavodoxins (Fld). The first example was described in 2008 when it was found that the butyryl-CoA dehydrogenase-electron-transferring flavoprotein complex (Bcd-EtfAB) of couples the endergonic reduction of ferredoxin (E' = -420 mV) with NADH (-320 mV) to the exergonic reduction of crotonyl-CoA to butyryl-CoA (-10 mV) with NADH. The discovery was followed by the finding of an electron-bifurcating Fd- and NAD-dependent [FeFe]-hydrogenase (HydABC) in (2009), Fd-dependent transhydrogenase (NfnAB) in various bacteria and archaea (2010), Fd- and H-dependent heterodisulfide reductase (MvhADG-HdrABC) in methanogenic archaea (2011), Fd- and NADH-dependent caffeyl-CoA reductase (CarCDE) in (2013), Fd- and NAD-dependent formate dehydrogenase (HylABC-FdhF2) in (2013), Fd- and NADP-dependent [FeFe]-hydrogenase (HytA-E) in (2013), Fd(?)- and NADH-dependent methylene-tetrahydrofolate reductase (MetFV-HdrABC-MvhD) in (2014), Fd- and NAD-dependent lactate dehydrogenase (LctBCD) in (2015), Fd- and FH-dependent heterodisulfide reductase (HdrA2B2C2) in (2017), and Fd- and NADH-dependent ubiquinol reductase (FixABCX) in (2017). The electron-bifurcating flavoprotein complexes known to date fall into four groups that have evolved independently, namely those containing EtfAB (CarED, LctCB, FixBA) with bound FAD, a NuoF homolog (HydB, HytB, or HylB) harboring FMN, NfnB with bound FAD, or HdrA harboring FAD. All these flavoproteins are cytoplasmic except for the membrane-associated protein FixABCX. The organisms-in which they have been found-are strictly anaerobic microorganisms except for the aerobe . The electron-bifurcating complexes are involved in a variety of processes such as butyric acid fermentation, methanogenesis, acetogenesis, anaerobic lactate oxidation, dissimilatory sulfate reduction, anaerobic- dearomatization, nitrogen fixation, and CO fixation. They contribute to energy conservation via the energy-converting ferredoxin: NAD reductase complex Rnf or the energy-converting ferredoxin-dependent hydrogenase complex Ech. This Review describes how this mechanism was discovered.
PubMed: 29593673
DOI: 10.3389/fmicb.2018.00401