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Scientific Reports May 2023Pomegranate crops are prone to wilt complex disease, which is known to severely hamper the crop yield. There have been limited studies that have explored...
Pomegranate crops are prone to wilt complex disease, which is known to severely hamper the crop yield. There have been limited studies that have explored bacteria-plant-host associations in wilt complex disease affecting pomegranate crops. In the present study, wilt infected rhizosphere soil samples (ISI, ASI) in pomegranate were studied in comparison to a healthy control (HSC). The 16S metagenomics sequencing approach using the MinION platform was employed for screening of bacterial communities and predictive functional pathways. Altered physicochemical properties in the soil samples were recorded showing a comparatively acidic pH in the ISI (6.35) and ASI (6.63) soil samples to the HSC soil (7.66), along with higher electrical conductivity in the ISI (139.5 µS/cm), ASI soil (180 µS/cm), HSC soil sample (123.33 µS/cm). While concentration of micronutrients such as Cl and B were significantly higher in the ISI and ASI soil as compared to the HSC, Cu and Zn were significantly higher in the ASI soil. The effectiveness and accuracy of 16S metagenomics studies in identifying beneficial and pathogenic bacterial communities in multi-pathogen-host systems depend on the completeness and consistency of the available 16S rRNA sequence repositories. Enhancing these repositories could significantly improve the exploratory potential of such studies. Thus, multiple 16S rRNA data repositories (RDP, GTDB, EzBioCloud, SILVA, and GreenGenes) were benchmarked, and the findings indicated that SILVA yields the most reliable matches. Consequently, SILVA was chosen for further analysis at the species level. Relative abundance estimates of bacterial species showed variations of growth promoting bacteria, namely, Staphylococcus epidermidis, Bacillus subtilis, Bacillus megatarium, Pseudomonas aeruginosa, Pseudomonas putida, Pseudomonas stutzeri and Micrococcus luteus. Functional profiling predictions employing PICRUSt2 revealed a number of enriched pathways such as transporter protein families involved in signalling and cellular processes, iron complex transport system substrate binding protein, peptidoglycan biosynthesis II (staphylococci) and TCA cycle VII (acetate-producers). In line with past reports, results suggest that an acidic pH along with the bioavailability of micronutrients such as Fe and Mn could be facilitating the prevalence and virulence of Fusarium oxysporum, a known causative pathogen, against the host and beneficial bacterial communities. This study identifies bacterial communities taking into account the physicochemical and other abiotic soil parameters in wilt-affected pomegranate crops. The insights obtained could be instrumental in developing effective management strategies to enhance crop yield and mitigate the impact of wilt complex disease on pomegranate crops.
Topics: Soil; Pomegranate; RNA, Ribosomal, 16S; Rhizosphere; Bacteria; Soil Microbiology; Plant Diseases
PubMed: 37244920
DOI: 10.1038/s41598-023-35219-z -
Metabolites May 2023Plant growth-promoting rhizobacteria (PGPR) can colonize plant root surfaces or form biofilms to promote plant growth and enhance plant resistance to harsh external...
Plant growth-promoting rhizobacteria (PGPR) can colonize plant root surfaces or form biofilms to promote plant growth and enhance plant resistance to harsh external environments. However, plant-PGPR interactions, especially chemical signaling molecules, are poorly understood. This study aimed to gain an in-depth understanding of the rhizosphere interaction mechanisms between PGPR and tomato plants. This study found that inoculation with a certain concentration of significantly promoted tomato growth and induced significant changes in tomato root exudates. Furthermore, the root exudates significantly induced NRCB010 growth, swarming motility, and biofilm formation. In addition, the composition of the root exudates was analyzed, and four metabolites (methyl hexadecanoate, methyl stearate, 2,4-di-tert-butylphenol, and n-hexadecanoic acid) significantly related to the chemotaxis and biofilm formation of NRCB010 were screened. Further assessment showed that these metabolites positively affected the growth, swarming motility, chemotaxis, or biofilm formation of strain NRCB010. Among these, n-hexadecanoic acid induced the most remarkable growth, chemotactic response, biofilm formation, and rhizosphere colonization. This study will help develop effective PGPR-based bioformulations to improve PGPR colonization and crop yields.
PubMed: 37233705
DOI: 10.3390/metabo13050664 -
Bioscience, Biotechnology, and... Jul 2023d-Aldotetroses are rare sugars that are obtained via chemical synthesis in low yield. In this study, we demonstrated that d-aldotetroses could be produced using 3...
d-Aldotetroses are rare sugars that are obtained via chemical synthesis in low yield. In this study, we demonstrated that d-aldotetroses could be produced using 3 isomerases. First, l-erythrulose was epimerized using d-tagatose 3-epimerase from Pseudomonas cichorii ST-24. The specific optical rotation of the reaction solution gradually decreased to zero, indicating that approximately 50% of the l-erythrulose was converted to d-erythrulose. d, l-Erythrulose mixture was isomerized with d-arabinose isomerase from Klebsiella pneumoniae 40bXX to produce d-threose, resulting in a conversion rate of 9.35%. d-Erythrose production using l-rhamnose isomerase from Pseudomonas stutzeri LL172 resulted in a conversion rate of 12.9%. Because of the low purity of the purchased d-erythrose, the product was reduced by the Raney nickel catalyst compared with authentic erythritol. We confirmed the products using HPLC and 13C-NMR spectra. This is the first report of d-aldotetrose production using an enzymatic reaction.
Topics: Tetroses; Hexoses; Isomerases; Aldose-Ketose Isomerases; Racemases and Epimerases
PubMed: 37156528
DOI: 10.1093/bbb/zbad058 -
Journal of Hazardous Materials Jul 2023Dissolved organic matter (DOM) play critical roles in arsenic (As) biotransformation in groundwater, but its compositional characteristics and interactions with...
Dissolved organic matter (DOM) play critical roles in arsenic (As) biotransformation in groundwater, but its compositional characteristics and interactions with indigenous microbial communities remain unclear. In this study, DOM signatures coupled with taxonomy and functions of microbial community were characterized in As-enriched groundwater by excitation-emission matrix, Fourier transform ion cyclotron resonance mass spectrometry and metagenomic sequencing. Results showed that As concentrations were significantly positively correlated with DOM humification (r = 0.707, p < 0.01) and the most dominant humic acid-like DOM components (r = 0.789, p < 0.01). Molecular characterization further demonstrated high DOM oxidation degree, with the prevalence of unsaturated oxygen-low aromatics, nitrogen (N/N)-containing compounds and unique CHO molecules in high As groundwater. These DOM properties were consistent with microbial composition and functional potentials. Both taxonomy and binning analyses demonstrated the dominance of Pseudomonas stutzeri, Microbacterium and Sphingobium xenophagum in As-enriched groundwater which possessed abundant As-reducing gene, with organic carbon degrading genes capable of labile to recalcitrant compounds degradation and high potentials of organic nitrogen mineralization to generate ammonium. Besides, most assembled bins in high As groundwater presented strong fermentation potentials which could facilitate carbon utilization by heterotrophic microbes. This study provides better insight into the potential role of DOM mineralization for As release in groundwater system.
Topics: Dissolved Organic Matter; Arsenic; Groundwater; Carbon; Microbiota; Nitrogen
PubMed: 37148792
DOI: 10.1016/j.jhazmat.2023.131566 -
Microbial Cell Factories May 2023Biological nitrogen fixation converting atmospheric dinitrogen to ammonia is an important way to provide nitrogen for plants. Pseudomonas stutzeri DSM4166 is a...
Systematic identification of endogenous strong constitutive promoters from the diazotrophic rhizosphere bacterium Pseudomonas stutzeri DSM4166 to improve its nitrogenase activity.
BACKGROUND
Biological nitrogen fixation converting atmospheric dinitrogen to ammonia is an important way to provide nitrogen for plants. Pseudomonas stutzeri DSM4166 is a diazotrophic Gram-negative bacterium isolated from the rhizosphere of cereal Sorghum nutans. Endogenous constitutive promoters are important for engineering of the nitrogen fixation pathway, however, they have not been systematically characterized in DSM4166.
RESULTS
Twenty-six candidate promoters were identified from DSM4166 by RNA-seq analysis. These 26 promoters were cloned and characterized using the firefly luciferase gene. The strengths of nineteen promoters varied from 100 to 959% of the strength of the gentamicin resistance gene promoter. The strongest P12445 promoter was used to overexpress the biological nitrogen fixation pathway-specific positive regulator gene nifA. The transcription level of nitrogen fixation genes in DSM4166 were significantly increased and the nitrogenase activity was enhanced by 4.1 folds determined by the acetylene reduction method. The nifA overexpressed strain produced 359.1 µM of extracellular ammonium which was 25.6 times higher than that produced by the wild-type strain.
CONCLUSIONS
The endogenous strong constitutive promoters identified in this study will facilitate development of DSM4166 as a microbial cell factory for nitrogen fixation and production of other useful compounds.
Topics: Pseudomonas stutzeri; Rhizosphere; Nitrogen Fixation; Nitrogen; Nitrogenase; Bacterial Proteins; Gene Expression Regulation, Bacterial
PubMed: 37138314
DOI: 10.1186/s12934-023-02085-3 -
Archives of Razi Institute Oct 2022Psoriasis is an autoimmune, persistent, inflammatory skin illness that is influenced by a variety of circumstances. Psoriasis etiology is strongly linked to bacteria,...
Psoriasis is an autoimmune, persistent, inflammatory skin illness that is influenced by a variety of circumstances. Psoriasis etiology is strongly linked to bacteria, particularly those in the pharynx and skin. This research intended to deepen our understanding by elucidating the connection between the skin microbiome and psoriasis to improve therapeutic balance using probiotics, antimicrobials, and even topical microbiota transplantation. In this work, the culture-dependent approach is utilized to compare the skin microbiomes of psoriatic and healthy individuals. On brane-heart infusion agar, swabs from 60 psoriasis patients in the flare-up stag and 40 healthy controls were cultured and grown for 48 hours. The resultant colonies were then subcultured and purified to produce a single pure colony. Using Macconkey agar for preliminary colony identification, Vitek then characterized the purified colonies. The results revealed substantial bacterial species and phyla variations between psoriatic patients and healthy controls. In addition, increased rates of opportunistic infections and were detected in psoriatic patients' normal skin and lesions.
Topics: Adult; Female; Humans; Male; Agar; Bacteria; Culture Media; Psoriasis; Skin
PubMed: 37123117
DOI: 10.22092/ARI.2022.359398.2414 -
Water Science and Technology : a... Apr 2023Previous study has shown that co-culturing acetogenic bacterium Sporomusa ovata (SO), with denitrifying bacterium Pseudomonas stutzeri (PS), is a promising strategy to...
Development of a mathematical model for a microbial denitrification co-culture system comprising acetogenic bacterium Sporomusa ovata and denitrifying bacterium Pseudomonas stutzeri.
Previous study has shown that co-culturing acetogenic bacterium Sporomusa ovata (SO), with denitrifying bacterium Pseudomonas stutzeri (PS), is a promising strategy to enhance the microbial denitrification for nitrate-contaminated groundwater remediation. However, the mutual effects and reaction kinetics of these two bacteria in the co-culture system are poorly understood. In this study, a mathematical model for this co-culture system was established to fill this knowledge gap. Model simulation demonstrated that SO had a significant effect on the kinetics of denitrification by PS, while PS slightly affected the kinetics of acetate production by SO. The optimal initial HCO/NO ratio and SO/PS inoculation ratio were 0.77-1.48 and 67 for the co-culture system to achieve satisfied denitrification performance with less acetate accumulation. Finally, the minimum hydrogen supply was recommended when the initial bicarbonate and nitrate concentrations were assigned in the range of 2-20 mM and 2-4 mM for simulating the natural nitrate-contaminated groundwater treatment. These findings could provide useful insights to guide the operation and optimization of the denitrification co-culture system.
Topics: Pseudomonas stutzeri; Nitrates; Denitrification; Coculture Techniques; Bacteria; Acetates; Models, Theoretical
PubMed: 37119171
DOI: 10.2166/wst.2023.110 -
Journal of Agricultural and Food... May 2023The plant root is a key pathway to absorb insecticides from soil and is colonized by beneficial and pathogenic microbial communities. Our study demonstrated that...
The plant root is a key pathway to absorb insecticides from soil and is colonized by beneficial and pathogenic microbial communities. Our study demonstrated that colonizing roots by nitrogen-fixing bacterium and pathogenic and increased the uptake of insecticides into maize roots from soil. An alteration in the permeability of root cells contributed to this increased uptake. For the subsequent root-to-shoot translocation, the relationship between translocation and log of the compound satisfied a Gaussian distribution. Relatively beneficial can promote maize seedling growth and increase translocation, whereas and pathogens can retard the seedling growth and reduce the translocation. Furthermore, the relationship between the concentration difference (difference of an insecticide from inoculation treatment to control) and log also showed a Gaussian distribution. The maximum concentration difference from the Gaussian equation can be applied to assess the capacity of rhizosphere microorganisms to influence translocation.
Topics: Rhizosphere; Seedlings; Zea mays; Plant Roots; Insecticides; Soil; Organic Chemicals; Soil Microbiology
PubMed: 37097808
DOI: 10.1021/acs.jafc.3c00140 -
Environmental Research Jul 2023Biodegradation, harnessing the metabolic versatility of microorganisms to reduce agrochemical contaminations, is commonly studied with enriched planktonic cells but...
Biodegradation, harnessing the metabolic versatility of microorganisms to reduce agrochemical contaminations, is commonly studied with enriched planktonic cells but overlooking the dominant lifestyle of microorganisms is to form biofilms, which compromises the efficiency of biodegradation in natural environment. Here, we employed a carbofuran-degrading bacterium Pseudomonas stutzeri PS21 to investigate how the bacterial biofilms formed and responded to agrochemicals. First, the PS21 biofilms formed with a core of bacterial cells enclosing with extracellular polymeric substances (EPSs), and the biofilms were active and resilient when exposed to carbofuran (up to 50 mg L). The formation was regulated by the second messenger bis-(3'-5')-cyclic di-guanosine monophosphate signaling, which strengthened the structural resistance and metabolic basis of biofilms to remain the degrading efficiency as comparable as the planktonic cells. Second, carbofuran distributed heterogeneously in the near-biofilm microenvironment via the covalent adsorption of biofilms, which provided a spontaneous force that enhanced the combination of carbofuran with biofilms to maintain high degrading activity. Additionally, we elucidated the biodegradation was driven by the integrated metabolic system of biofilms involving the extracellular enzymes located in the EPSs. This study exhibited the structural and metabolic advantages of microbial biofilms, highlighting the attractive potentials of exploring biofilm-based strategies to facilitate the in-situ bioremediation of organic contaminations.
Topics: Biodegradation, Environmental; Pseudomonas stutzeri; Carbofuran; Biofilms; Extracellular Polymeric Substance Matrix; Bacteria
PubMed: 37068725
DOI: 10.1016/j.envres.2023.115894 -
Waste Management (New York, N.Y.) Jun 2023The extensive distribution of microplastics and their abundance around the world has raised a global concern because of the lack of proper disposal channels as well as...
The extensive distribution of microplastics and their abundance around the world has raised a global concern because of the lack of proper disposal channels as well as poor knowledge of their implications on human health. Sustainable remediation techniques are required owing to the absence of proper disposal methods. The present study explores the deterioration process of high-density polyethylene (HDPE) microplastics using various microbes along with the kinetics and modeling of the process using multiple non-linear regression models. Ten different microbial strains were used for the degradation of microplastics for a period of 30 days. Effect of process parameters on the degradation process was studied with the selected five microbial strains that presented the best degradation results. The reproducibility and efficacy of the process were tested for an extended period of 90 days. Fourier-transform infrared spectroscopy (FTIR) and field emission-scanning electron microscopy (FE-SEM) were used for the analysis of microplastics. Polymer reduction and half-life were evaluated. Pseudomonas putida achieved the maximum degradation efficiency of 12.07% followed by Rhodococcus ruber (11.36%), Pseudomonas stutzeri (8.28%), Bacillus cereus (8.26%), and Brevibacillus borstelensis (8.02%) after 90 days. Out of 14 models tested, 5 were found capable of modeling the process kinetics and based on simplicity and statistical data, Modified Michaelis-Menten model (F8; R = 0.97) was selected as superior to others. This study successfully establishes the potential of bioremediation of microplastics as the viable process.
Topics: Humans; Microplastics; Polyethylene; Plastics; Reproducibility of Results; Kinetics; Water Pollutants, Chemical; Spectroscopy, Fourier Transform Infrared
PubMed: 37059038
DOI: 10.1016/j.wasman.2023.04.002