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Frontiers in Microbiology 2023() has been found principally in oil-polluted environments. The capability of to thrive from the degradation of pollutant compounds makes it a species of interest for...
() has been found principally in oil-polluted environments. The capability of to thrive from the degradation of pollutant compounds makes it a species of interest for potential bioremediation applications. However, little has been reported about the diversity of . In this study, genome sequences of strains from different origins were analyzed, revealing that it is a diverse species with an open pan-genome that will continue revealing new genes and functionalities as the genomes of more strains are sequenced. The nucleotide signatures and intra- and inter-species variation of the 16S rRNA genes of were reevaluated. A strategy of screening 16S rRNA gene sequences in public databases enabled the detection of 158 additional strains, of which only 23% were described as . The species was detected from a wide range of environments, although mostly from aquatic and polluted environments, predominantly related to petroleum oil. Genomic and phenotypic analyses confirmed that possesses varied inherent capabilities for aromatic compounds degradation. This study increases the knowledge of the biology and diversity of and will serve as a basis for future work with the species.
PubMed: 37275147
DOI: 10.3389/fmicb.2023.1159176 -
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 -
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 -
Materials (Basel, Switzerland) Apr 2023Microbiologically influenced corrosion (MIC) is a common phenomenon in water treatment, shipping, construction, marine and other industries. Sulfate-reducing bacteria...
Microbiologically influenced corrosion (MIC) is a common phenomenon in water treatment, shipping, construction, marine and other industries. Sulfate-reducing bacteria (SRB) often lead to MIC. In this paper, a strain of () with the ability to inhibit SRB corrosion is isolated from the soil through enrichment culture. is a short, rod-shaped, white and transparent colony with denitrification ability. Our 16SrDNA sequencing results verify the properties of strains. The growth conditions of bacteria and SRB are similar, and the optimal culture conditions are about 30 °C, pH 7, and the stable stage is reached in about seven days. The bacteria can coexist in the same growth environment. Using the weight loss method, electrochemical experiments and composition analysis techniques we found that can inhibit the corrosion of X70 steel by SRB at 20~40 °C, pH 6~8. Furthermore, long-term tests at 3, 6 and 9 months reveal that can effectively inhibit the corrosion of X70 steel caused by SRB.
PubMed: 37049190
DOI: 10.3390/ma16072896 -
Synthetic and Systems Biotechnology Jun 2023The biological treatment of wastewater with high concentrations of ammonia nitrogen has become a hot research issue, but there are limited reports on the mechanism of...
The biological treatment of wastewater with high concentrations of ammonia nitrogen has become a hot research issue, but there are limited reports on the mechanism of ammonia nitrogen utilization by microorganisms. In this paper, a transcriptomic approach was used to investigate the differences in gene expression at 500.0 mg/L (Amo 500) and 100.0 mg/L (Amo 100) ammonium concentrations to reveal the mechanism of ammonia nitrogen removal from water by F2. The transcriptome data showed 1015 (459 up-regulated and 556 down-regulated) differentially expressed genes with functional gene annotation related to nitrogen source metabolism, glycolysis, tricarboxylic acid cycle, extracellular polysaccharide synthesis, energy conversion and transmembrane transport, revealing the metabolic process of ammonium nitrogen conversion to biological nitrogen in F2 through assimilation. To verify the effect of ammonium transporter protein (AmtB) of cell membrane on assimilation, a F2-Δ mutant strain was obtained by constructing a knockout plasmid (pK18mobsacB-Δ), and it was found that the growth characteristics and ammonium removal rate of the mutant strain were significantly reduced at high ammonium concentration. The carbon source components and dissolved oxygen conditions were optimized after analyzing the transcriptome data, and the ammonium removal rate was increased from 41.23% to 94.92% with 500.0 mg/L ammonium concentration. The study of F2 transcript level reveals the mechanism of ammonia nitrogen influence on microbial assimilation process and improvement strategy, which provides a new strategy for the treatment of ammonia nitrogen wastewater.
PubMed: 37033292
DOI: 10.1016/j.synbio.2023.03.002 -
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 -
Journal of Food Protection Apr 2023In Mexico, bullfrogs (Lithobates catesbeianus) are produced as gourmet food. However, bullfrogs can be carriers of pathogens because the frogs' preferred living...
In Mexico, bullfrogs (Lithobates catesbeianus) are produced as gourmet food. However, bullfrogs can be carriers of pathogens because the frogs' preferred living conditions occur in stagnant water. The present study aimed to identify bacteria that cause foodborne diseases or are associated with human diseases. For molecular identification, based on the sequential analysis by 16S rRNA or rpoD was conducted on all isolates obtained from bullfrog. A total of 91 bacterial isolates were obtained from bullfrogs; 14 genera and 23 species were identified, including Acinetobacter johnsonii 16.5%; Aeromonas media 14.3%; Aeromonas veronii 13.2%; Providencia rettgeri 7.7%; Citrobacter freundii 6.6%; Aeromonas caviae 4.4%; Aeromonas hydrophila and Elizabethkingia ursingii 3.3%; Pseudomonas stutzeri, Raoultella ornithinolytica, and Shewanella putrefaciens 2.2%; Acinetobacter guillouiae, Acinetobacter pseudolwoffii, Citrobacter portucalensis, Citrobacter werkmanii, Edwardsiella anguillarum, Klebsiella michiganensis, Kluyvera intermedia, Kocuria rosea, Myroides odoratimimus, Myroides odoratus, Proteus sp., and Proteus hauseri 1.1%. In this study, 49.4% of the isolates obtained cause foodborne disease, 19.8% are bacteria that play an important role in the spoilage of food, 5.5% of isolates have nosocomial significance, 13.2% of bacteria are considered to be pollutants of the ecosystem, and in the case of A. salmonicida and Edwardsiella anguillarum (12.1%) to have a negative impact on aquaculture. Acinetobacter pseudolwoffii and Citrobacter portucalensis have not been reported to cause disease. Lastly of these isolates, 97.8% (89/91) can cause disease by food consumption or by direct contact for immunocompromised persons. The presence of these bacteria in bullfrogs represents a significant problem for human health. There is evidence that these microorganisms are pathogenic and frogs may also be reservoirs.
Topics: Animals; Humans; Rana catesbeiana; Ecosystem; RNA, Ribosomal, 16S; Foodborne Diseases
PubMed: 36948016
DOI: 10.1016/j.jfp.2023.100067 -
Microbiology Spectrum Mar 2023One of the major challenges for the bioremediation application of microbial nitrous oxide (NO) reduction is its oxygen sensitivity. While a few strains were reported...
One of the major challenges for the bioremediation application of microbial nitrous oxide (NO) reduction is its oxygen sensitivity. While a few strains were reported capable of reducing NO under aerobic conditions, the NO reduction kinetics of phylogenetically diverse NO reducers are not well understood. Here, we analyzed and compared the kinetics of clade I and clade II NO-reducing bacteria in the presence or absence of oxygen (O) by using a whole-cell assay with NO and O microsensors. Among the seven strains tested, NO reduction of Stutzerimonas stutzeri TR2 and ZoBell was not inhibited by oxygen (i.e., oxygen tolerant). Paracoccus denitrificans, Azospirillum brasilense, and Gemmatimonas aurantiaca reduced NO in the presence of O but slower than in the absence of O (i.e., oxygen sensitive). NO reduction of Pseudomonas aeruginosa and Dechloromonas aromatica did not occur when O was present (i.e., oxygen intolerant). Amino acid sequences and predicted structures of NosZ were highly similar among these strains, whereas oxygen-tolerant NO reducers had higher oxygen consumption rates. The results suggest that the mechanism of O tolerance is not directly related to NosZ structure but is rather related to the scavenging of O in the cells and/or accessory proteins encoded by the cluster. Some bacteria can reduce NO in the presence of O, whereas others cannot. It is unclear whether this trait of aerobic NO reduction is related to the phylogeny and structure of NO reductase. The understanding of aerobic NO reduction is critical for guiding emission control, due to the common concurrence of NO and O in natural and engineered systems. This study provided the NO reduction kinetics of various bacteria under aerobic and anaerobic conditions and classified the bacteria into oxygen-tolerant, -sensitive, and -intolerant NO reducers. Oxygen-tolerant NO reducers rapidly consumed O, which could help maintain the low O concentration in the cells and keep their NO reductase active. These findings are important and useful when selecting NO reducers for bioremediation applications.
PubMed: 36926990
DOI: 10.1128/spectrum.04709-22