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NPJ Biofilms and Microbiomes Jul 2021Biofilm and nitrogen fixation are two competitive strategies used by many plant-associated bacteria; however, the mechanisms underlying the formation of nitrogen-fixing...
Biofilm and nitrogen fixation are two competitive strategies used by many plant-associated bacteria; however, the mechanisms underlying the formation of nitrogen-fixing biofilms remain largely unknown. Here, we examined the roles of multiple signalling systems in the regulation of biofilm formation by root-associated diazotrophic P. stutzeri A1501. Physiological analysis, construction of mutant strains and microscale thermophoresis experiments showed that RpoN is a regulatory hub coupling nitrogen fixation and biofilm formation by directly activating the transcription of pslA, a major gene involved in the synthesis of the Psl exopolysaccharide component of the biofilm matrix and nifA, the transcriptional activator of nif gene expression. Genetic complementation studies and determination of the copy number of transcripts by droplet digital PCR confirmed that the regulatory ncRNA RsmZ serves as a signal amplifier to trigger biofilm formation by sequestering the translational repressor protein RsmA away from pslA and sadC mRNAs, the latter of which encodes a diguanylate cyclase that synthesises c-di-GMP. Moreover, RpoS exerts a braking effect on biofilm formation by transcriptionally downregulating RsmZ expression, while RpoS expression is repressed posttranscriptionally by RsmA. These findings provide mechanistic insights into how the Rpo/Gac/Rsm regulatory networks fine-tune nitrogen-fixing biofilm formation in response to the availability of nutrients.
Topics: Bacterial Proteins; Biofilms; Gene Expression Regulation, Bacterial; Gene Order; Gene Regulatory Networks; Nitrogen Fixation; Nitrogenase; Pseudomonas stutzeri; Repetitive Sequences, Nucleic Acid; Transcriptional Activation
PubMed: 34210981
DOI: 10.1038/s41522-021-00230-7 -
PloS One 2022Two-component systems (TCSs) are widespread regulatory systems in bacteria, which control cellular functions and play an important role in sensing various external...
Two-component systems (TCSs) are widespread regulatory systems in bacteria, which control cellular functions and play an important role in sensing various external stimuli and regulating gene expression in response to environmental changes. Among the nineteen genes for the two-component system found in the whole genome of Pseudomonas stutzeri LH-42, one of the TCS coded by the HK-1 gene, has a structural domain similar to the HAMP domain, which plays an important role in regulating bacterial virulence in other bacteria. In this study, the deletion mutant LH-42△HK-1 was successfully constructed using the lambda Red recombinase system. Compared with the wild-type strain, the mutant strain LH-42△HK-1 showed a significantly slower growth time and a longer stationary phase time. In addition, in the plate bacteriostatic experiment with Escherichia coli DH5α as an indicator strain, the inhibition zone size of the mutant strain showed significantly less than the wild-type strain(P<0.05), indicating that the virulence of the mutant strain was significantly reduced compared with the wild-type strain. Overall, the results indicate that the deletion of the gene HK-1 decreased bacterial virulence in Pseudomonas stutzeri LH-42.
Topics: Humans; Pseudomonas stutzeri; Virulence; Bone Plates; Escherichia coli; Escherichia coli Infections
PubMed: 36445858
DOI: 10.1371/journal.pone.0277089 -
BMC Microbiology Jun 2021A bacterial consortium SCP comprising three bacterial members, viz. Stenotrophomonas acidaminiphila APG1, Pseudomonas stutzeri APG2 and Cellulomonas sp. APG4 was...
BACKGROUND
A bacterial consortium SCP comprising three bacterial members, viz. Stenotrophomonas acidaminiphila APG1, Pseudomonas stutzeri APG2 and Cellulomonas sp. APG4 was developed for degradation of the mono-azo dye, Reactive Blue 28. The genomic analysis of each member of the SCP consortium was done to elucidate the catabolic potential and role of the individual organism in dye degradation.
RESULTS
The genes for glycerol utilization were detected in the genomes of APG2 and APG4, which corroborated with their ability to grow on a minimal medium containing glycerol as the sole co-substrate. The genes for azoreductase were identified in the genomes of APG2 and APG4, while no such trait could be determined in APG1. In addition to co-substrate oxidation and dye reduction, several other cellular functions like chemotaxis, signal transduction, stress-tolerance, repair mechanisms, aromatic degradation, and copper tolerance associated with dye degradation were also annotated. A model for azo dye degradation is postulated, representing the predominant role of APG4 and APG2 in dye metabolism while suggesting an accessory role of APG1.
CONCLUSIONS
This exploratory study is the first-ever attempt to divulge the genetic basis of azo-dye co-metabolism by cross-genome comparisons and can be harnessed as an example for demonstrating microbial syntrophy.
Topics: Azo Compounds; Biodegradation, Environmental; Cellulomonas; Coloring Agents; Culture Media; Genome, Bacterial; Microbial Consortia; Pseudomonas stutzeri; Stenotrophomonas
PubMed: 34116639
DOI: 10.1186/s12866-021-02236-9 -
Microorganisms Dec 2021Fish gut represents a peculiar ecological niche where bacteria can transit and reside to play vital roles by producing bio-compounds with nutritional, immunomodulatory...
Fish gut represents a peculiar ecological niche where bacteria can transit and reside to play vital roles by producing bio-compounds with nutritional, immunomodulatory and other functions. This complex microbial ecosystem reflects several factors (environment, feeding regimen, fish species, etc.). The objective of the present study was the identification of intestinal microbial strains able to produce molecules called biosurfactants (BSs), which were tested for surface and antibacterial activity in order to select a group of probiotic bacteria for aquaculture use. Forty-two bacterial isolates from the digestive tracts of twenty Mediterranean grey mullets were screened for testing emulsifying (E-24), surface and antibiotic activities. Fifty percent of bacteria, ascribed to , sp., and and were found to be surfactant producers. Of the tested strains, 26.6% exhibited an antibacterial activity against (10.0 ± 0.0-14.5 ± 0.7 mm inhibition zone), and among them, 23.3% of isolates also showed inhibitory activity vs. (10.0 ± 0.0-18.5 ± 0.7 mm inhibition zone) and 6.6% vs. (11.5 ± 0.7-17.5 ± 0.7 mm inhibition zone). According to preliminary chemical analysis, the bioactive compounds are suggested to be ascribed to the class of glycolipids. This works indicated that fish gut is a source of bioactive compounds which deserves to be explored.
PubMed: 34946156
DOI: 10.3390/microorganisms9122555 -
Microorganisms Apr 2020Pseudomonas stutzeri A1501 possesses an extraordinary number of transporters which confer this rhizosphere bacterium with the sophisticated ability to metabolize various...
Pseudomonas stutzeri A1501 possesses an extraordinary number of transporters which confer this rhizosphere bacterium with the sophisticated ability to metabolize various carbon sources. However, sugars are not a preferred carbon source for P. stutzeri A1501. The P. stutzeri A1501 genome has been sequenced, allowing for the homology-based in silico identification of genes potentially encoding sugar-transport systems by using established microbial sugar transporters as a template sequence. Genomic analysis revealed that there were 10 sugar transporters in P. stutzeri A1501, most of which belong to the ATP-binding cassette (ABC) family (5/10); the others belong to the phosphotransferase system (PTS), major intrinsic protein (MIP) family, major facilitator superfamily (MFS) and the sodium solute superfamily (SSS). These systems might serve for the import of glucose, galactose, fructose and other types of sugar. Growth analysis showed that the only effective medium was glucose and its corresponding metabolic system was relatively complete. Notably, the loci of glucose metabolism regulatory systems HexR, GltR/GtrS, and GntR were adjacent to the transporters ABC, ABC, and ABC, respectively. Only the ABC expression was significantly upregulated under both glucose-sufficient and -limited conditions. The predicted structure and mutant phenotype data of the key protein GtsA provided biochemical evidence that P. stutzeri A1501 predominantly utilized the ABC transporter for glucose uptake. We speculate that gene absence and gene diversity in P. stutzeri A1501 was caused by sugar-deficient environmental factors and hope that this report can provide guidance for further analysis of similar bacterial lifestyles.
PubMed: 32325908
DOI: 10.3390/microorganisms8040592 -
Plant Biotechnology Journal Jan 2021High-temperature bioconversion of lignocellulose into fermentable sugars has drawn attention for efficient production of renewable chemicals and biofuels, because...
High-temperature bioconversion of lignocellulose into fermentable sugars has drawn attention for efficient production of renewable chemicals and biofuels, because competing microbial activities are inhibited at elevated temperatures and thermostable cell wall degrading enzymes are superior to mesophilic enzymes. Here, we report on the development of a platform to produce four different thermostable cell wall degrading enzymes in the chloroplast of Chlamydomonas reinhardtii. The enzyme blend was composed of the cellobiohydrolase CBM3GH5 from C. saccharolyticus, the β-glucosidase celB from P. furiosus, the endoglucanase B and the endoxylanase XynA from T. neapolitana. In addition, transplastomic microalgae were engineered for the expression of phosphite dehydrogenase D from Pseudomonas stutzeri, allowing for growth in non-axenic media by selective phosphite nutrition. The cellulolytic blend composed of the glycoside hydrolase (GH) domain GH12/GH5/GH1 allowed the conversion of alkaline-treated lignocellulose into glucose with efficiencies ranging from 14% to 17% upon 48h of reaction and an enzyme loading of 0.05% (w/w). Hydrolysates from treated cellulosic materials with extracts of transgenic microalgae boosted both the biogas production by methanogenic bacteria and the mixotrophic growth of the oleaginous microalga Chlorella vulgaris. Notably, microalgal treatment suppressed the detrimental effect of inhibitory by-products released from the alkaline treatment of biomass, thus allowing for efficient assimilation of lignocellulose-derived sugars by C. vulgaris under mixotrophic growth.
Topics: Biofuels; Biomass; Chlorella vulgaris; Lignin; Microalgae
PubMed: 32649019
DOI: 10.1111/pbi.13447 -
Scientific Reports Jan 2024There has recently been an explosion of studies implicating the human microbiome in playing a critical role in many disease and wellness states. The etiology of abnormal... (Observational Study)
Observational Study
There has recently been an explosion of studies implicating the human microbiome in playing a critical role in many disease and wellness states. The etiology of abnormal semen analysis (SA) parameters is not identified in 30% of cases; investigations involving the semen microbiome may bridge this gap. Here, we explore the relationship between the semen microbiome and alterations of sperm parameters. We recruited men presenting for fertility evaluation or vasectomy consultation with proven biological paternity. SA and next generation sequencing was performed. Differential abundance testing using Analysis of composition of Microbiota with Bias Correction (ANCOM-BC) was performed along with canonical correlational analysis for microbial community profiling. Men with abnormal (N = 27) sperm motility showed a higher abundance of Lactobacillus iners compared to those with normal (N = 46) sperm motility (mean proportion 9.4% versus 2.6%, p = 0.046). This relationship persisted on canonical correlational analysis (r = 0.392, p = 0.011). Men with abnormal sperm concentration (N = 20) showed a higher abundance of Pseudomonas stutzeri (2.1% versus 1.0%, p = 0.024) and Pseudomonas fluorescens (0.9% versus 0.7%, p = 0.010), but a lower abundance of Pseudomonas putida (0.5% versus 0.8%, p = 0.020), compared to those with normal sperm concentration (N = 53). Major limitations are related to study design (cross-sectional, observational). Our results suggest that a small group of microorganisms may play a critical role in observed perturbations of SA parameters. Some of these microbes, most notably Lactobacillus iners, have been described extensively within other, fertility-related, contexts, whereas for others, this is the first report where they have potentially been implicated. Advances in our understanding of the semen microbiome may contribute to potentially new therapeutic avenues for correcting impairments in sperm parameters and improving male fertility.
Topics: Humans; Male; Cross-Sectional Studies; Fertility; Infertility, Male; Lactobacillus; Semen; Semen Analysis; Sperm Count; Sperm Motility; Spermatozoa
PubMed: 38212576
DOI: 10.1038/s41598-024-51686-4 -
Microorganisms Jul 2022is a recently proposed genus within the comprising strains in the formerly phylogenetic group of . At least sixteen named species have to be included in the genus,...
is a recently proposed genus within the comprising strains in the formerly phylogenetic group of . At least sixteen named species have to be included in the genus, together with 22 genomovars of . To clarify the taxonomy of , a core-genome phylogeny of 200 strains in the genus was inferred and monophyletic strains with average nucleotide identities (ANIb) with values equal to or higher than 95 were grouped in the same phylogenomic species. A total of 45 phylogenomic species within the genus were detected in the present study. Sixteen phylogenomic species correspond to already named species, although three of them are not yet validated and two are proposed in the present study. A synonymy was detected between and , both members of phylogenomic species 3, with a prevalence of the name. The correspondence of the phylogenomic species to the genome taxonomy database classification (GTDB taxonomy) is discussed. Combining phylogenomic and phenotypic data, two novel species are described ( and ) and two species descriptions are emended ( and ).
PubMed: 35889082
DOI: 10.3390/microorganisms10071363 -
Turkiye Parazitolojii Dergisi Sep 2019The aim of this study was to investigate the physical, chemical and microbiological contamination of indoor swimming pools.
OBJECTIVE
The aim of this study was to investigate the physical, chemical and microbiological contamination of indoor swimming pools.
METHODS
Pool water specimens were collected using a plastic polypropylene sterilized bottle. The physical and chemical qualities of the waters were analyzed in terms of temperature, turbidity, pH, and free residual chlorine, with the standard methods for the examination of water. Bacteriological (routine methods) and parasitological (molecular methods) tests were carried out on pools water.
RESULTS
The mean temperature, pH, and residual chlorine of the indoor pools were 31.2 °C, 7.6 and 1.5 mg/L, respectively. Turbidity was not observed in any of the pools. The pH and temperature values were in standard ranges in 92.3% and 15.4% of the waters of swimming pools, respectively. The prevalence rates of bacterial and amoebic contaminations of the water in the swimming pools were 53.8% and 46.2%, respectively. One pool (7.7%) was contaminated with both bacteria and amoeba. and spp. were isolated from the pool waters.
CONCLUSION
In this study, some microorganisms were identified from the water pools. Effective management of swimming pools and proper control of the physical, chemical and microbiological property of water pools can produce the healthy recreational activity.
Topics: Amoeba; Bacteria; Chlorine; Cross-Sectional Studies; Cryptosporidium; Hydrogen-Ion Concentration; Swimming Pools; Temperature; Water; Water Microbiology
PubMed: 31502803
DOI: 10.4274/tpd.galenos.2019.6112 -
Nature Communications Jun 2023Plasmids are the main vector by which antibiotic resistance is transferred between bacterial cells within surface-associated communities. In this study, we ask whether...
Plasmids are the main vector by which antibiotic resistance is transferred between bacterial cells within surface-associated communities. In this study, we ask whether there is an optimal time to administer antibiotics to minimize plasmid spread in new bacterial genotypes during community expansion across surfaces. We address this question using consortia of Pseudomonas stutzeri strains, where one is an antibiotic resistance-encoding plasmid donor and the other a potential recipient. We allowed the strains to co-expand across a surface and administered antibiotics at different times. We find that plasmid transfer and transconjugant proliferation have unimodal relationships with the timing of antibiotic administration, where they reach maxima at intermediate times. These unimodal relationships result from the interplay between the probabilities of plasmid transfer and loss. Our study provides mechanistic insights into the transfer and proliferation of antibiotic resistance-encoding plasmids within microbial communities and identifies the timing of antibiotic administration as an important determinant.
Topics: Anti-Bacterial Agents; Drug Resistance, Microbial; Genotype; Microbiota; Plasmids
PubMed: 37316482
DOI: 10.1038/s41467-023-39354-z