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MSphere May 2024The RNA chaperone Hfq acts as a global regulator of numerous biological processes, such as carbon/nitrogen metabolism and environmental adaptation in plant-associated...
UNLABELLED
The RNA chaperone Hfq acts as a global regulator of numerous biological processes, such as carbon/nitrogen metabolism and environmental adaptation in plant-associated diazotrophs; however, its target RNAs and the mechanisms underlying nitrogen fixation remain largely unknown. Here, we used enhanced UV cross-linking immunoprecipitation coupled with high-throughput sequencing to identify hundreds of Hfq-binding RNAs probably involved in nitrogen fixation, carbon substrate utilization, biofilm formation, and other functions. Collectively, these processes endow strain A1501 with the requisite capabilities to thrive in the highly competitive rhizosphere. Our findings revealed a previously uncharted landscape of Hfq target genes. Notable among these is , encoding an isomerase necessary for nitrogenase reductase solubility; , encoding an ammonium transporter; , encoding a carbohydrate porin; and , encoding a chemotaxis protein. Furthermore, we identified more than 100 genes of unknown function, which expands the potential direct regulatory targets of Hfq in diazotrophs. Our data showed that Hfq directly interacts with the mRNA of regulatory proteins (RsmA, AlgU, and NifA), regulatory ncRNA RsmY, and other potential targets, thus revealing the mechanistic links in nitrogen fixation and other metabolic pathways.
IMPORTANCE
Numerous experimental approaches often face challenges in distinguishing between direct and indirect effects of Hfq-mediated regulation. New technologies based on high-throughput sequencing are increasingly providing insight into the global regulation of Hfq in gene expression. Here, enhanced UV cross-linking immunoprecipitation coupled with high-throughput sequencing was employed to identify the Hfq-binding sites and potential targets in the root-associated A1501 and identify hundreds of novel Hfq-binding RNAs that are predicted to be involved in metabolism, environmental adaptation, and nitrogen fixation. In particular, we have shown Hfq interactions with various regulatory proteins' mRNA and their potential targets at the posttranscriptional level. This study not only enhances our understanding of Hfq regulation but, importantly, also provides a framework for addressing integrated regulatory network underlying root-associated nitrogen fixation.
PubMed: 38747590
DOI: 10.1128/msphere.00762-23 -
Data in Brief Jun 2024The sea cucumber () is a species found in the shallow waters near coral reefs and seagrass beds in Puerto Rico. To characterize the microbial taxonomic composition and...
The sea cucumber () is a species found in the shallow waters near coral reefs and seagrass beds in Puerto Rico. To characterize the microbial taxonomic composition and functional profiles present in the sea cucumber, total DNA was obtained from their intestinal system, fosmid libraries constructed, and subsequent sequencing was performed. The diversity profile displayed that the most predominant domain was Bacteria (76.56 %), followed by Viruses (23.24 %) and Archaea (0.04 %). Within the 11 phyla identified, the most abundant was Proteobacteria (73.16 %), followed by Terrabacteria group (3.20 %) and Fibrobacterota, Chlorobiota, Bacteroidota (FCB) superphylum (1.02 %). The most abundant species were (21.77 %), (14.78 %), and (5.00 %). The functional profile revealed that the most abundant functions are related to transporters, MISC (miscellaneous information systems), organic nitrogen, energy, and carbon utilization. The data collected in this project on the diversity and functional profiles of the intestinal system of the provided a detailed view of its microbial ecology. These findings may motivate comparative studies aimed at understanding the role of the microbiome in intestinal regeneration.
PubMed: 38690316
DOI: 10.1016/j.dib.2024.110421 -
Microbial Physiology Apr 2024Pseudomonas stutzeri KC can rapidly degrade carbon tetrachloride (CCl4) to CO2 by a fortuitous reaction with pyridine-2,6-bis(thiocarboxylic acid), a metal chelator...
Pseudomonas stutzeri KC can rapidly degrade carbon tetrachloride (CCl4) to CO2 by a fortuitous reaction with pyridine-2,6-bis(thiocarboxylic acid), a metal chelator encoded by pdt genes. These genes were first identified after a spontaneous mutant, strain CTN1, lost the ability to degrade CCl4. Here we report the complete genome of strain KC and show that these pdt genes are located on an integrative and conjugative element (ICE), designated ICEPsstKC. Comparative genome analyses revealed homologues of pdt genes in genomes of members of other gammaproteobacterial orders. Discrepancies between the tree topologies of the deduced pdt gene products and the host phylogeny based on 16S rRNA provided evidence for horizontal gene transfer (HGT) in several sequenced strains of these orders. In addition to ICEPsstKC, HGT may be have been facilitated by other mobile genetic elements, as indicated by the location of the pdt gene cluster adjacent to fragments of other ICEs and prophages in several genome assemblies. We could here show that the majority of cells from the culture collection DSMZ had lost the ICE. The presence of the pdt gene cluster on mobile genetic elements has important implications for the bioremediation of CCl4 for bioremediation of CCl4 and needs consideration when selecting suitable strains.
PubMed: 38626743
DOI: 10.1159/000538783 -
Heliyon Apr 2024Overuse of sulfonamides in aquaculture and agriculture leads to residual drugs that cause serious pollution of the environment. However, the residues of sulfonamides in...
Overuse of sulfonamides in aquaculture and agriculture leads to residual drugs that cause serious pollution of the environment. However, the residues of sulfonamides in the environment are not unique, and the existing microbial degradation technology has a relatively low degradation rate of sulfonamides. Therefore, in this study, a strain (DLY-21) with the ability to degrade four common SAs was screened and isolated from aerobic compost. Under optimal conditions, the DLY-21 strain degraded four sulfonamides simultaneously within 48 h, and the degradation rates were all over 90%, with the average degradation rates of SAs being sulfoxide (SDM) ≈ sulfachloropyridazine (SCP) > sulfa quinoxaline (SQ) > sulfadiazine (SQ). In addition, the main compounds of the strain DLY-21-degrading SAs were identified by LC-MS analysis. On this basis, four detailed reaction pathways for SA degradation were deduced. This is the first report of the use of a strain to degrade four sulfonamide antibiotics (SQ, SDM, SCP, and SM1), which can improve the removal efficiency of sulfonamide antibiotic pollutants and thus ameliorate environmental pollution. The results showed that DLY-21 had a good degradation effect on four SAs (SQ, SDM, SCP, and SM1).
PubMed: 38601639
DOI: 10.1016/j.heliyon.2024.e29123 -
Microbiology Spectrum May 2024Inoculation with plant growth-promoting rhizobacteria (PGPR) strains has promoted plant growth and decreased nitrous oxide (N₂O) emissions from agricultural soils...
UNLABELLED
Inoculation with plant growth-promoting rhizobacteria (PGPR) strains has promoted plant growth and decreased nitrous oxide (N₂O) emissions from agricultural soils simultaneously. However, limited PGPR strains can mitigate N₂O emissions from agricultural soils, and the microbial ecological mechanisms underlying N₂O mitigation after inoculation are poorly understood. In greenhouse pot experiments, the effects of inoculation with NRCB010 and NRCB025 on tomato growth and N₂O emissions were investigated in two vegetable agricultural soils with contrasting textures. Inoculation with NRCB010 and NRCB025 significantly promoted tomato growth in both soils. Moreover, inoculation with NRCB010 decreased the N₂O emissions from the fine- and coarse-textured soils by 38.7% and 52.2%, respectively, and inoculation with NRCB025 decreased the N₂O emissions from the coarse-textured soil by 76.6%. Inoculation with NRCB010 and NRCB025 decreased N₂O emissions mainly by altering soil microbial community composition and the abundance of nitrogen-cycle functional genes. The N₂O-mitigating effect might be partially explained by a decrease in the ()/(I + II) and ()/(I + II) ratios, respectively. Soil pH and organic matter were key variables that explain the variation in abundance of N-cycle functional genes and subsequent N₂O emission. Moreover, the N₂O-mitigating effect varied depending on soil textures and individual strain after inoculation. This study provides insights into developing biofertilizers with plant growth-promoting and N₂O-mitigating effects.
IMPORTANCE
Plant growth-promoting rhizobacteria (PGPR) have been applied to mitigate nitrous oxide (N₂O) emissions from agricultural soils, but the microbial ecological mechanisms underlying N₂O mitigation are poorly understood. That is why only limited PGPR strains can mitigate N₂O emissions from agricultural soils. Therefore, it is of substantial significance to reveal soil ecological mechanisms of PGPR strains to achieve efficient and reliable N₂O-mitigating effect after inoculation. Inoculation with strains decreased N₂O emissions from two soils with contrasting textures probably by altering soil microbial community composition and gene abundance involved in nitrification and denitrification. Our findings provide detailed insight into soil ecological mechanisms of PGPR strains to mitigate N₂O emissions from vegetable agricultural soils.
Topics: Soil Microbiology; Nitrous Oxide; Soil; Vegetables; Solanum lycopersicum; Microbiota; Pseudomonas stutzeri; Agriculture
PubMed: 38511949
DOI: 10.1128/spectrum.00186-24 -
Ecotoxicology and Environmental Safety Mar 2024Understanding the developmental characteristics of microbial communities in biofilms is crucial for designing targeted functional microbial enhancements for the...
Understanding the developmental characteristics of microbial communities in biofilms is crucial for designing targeted functional microbial enhancements for the remediation of complex contamination scenarios. The strong prioritization effect of microorganisms confers the ability to colonize strains that arrive first dominantly. In this study, the auto-aggregating denitrifying bacterial Pseudomonas stutzeri strain YC-34, which has both nitrogen and chromium removal characteristics, was used as a biological material to form a stable biofilm system based on the principle of dominant colonization and biofortification. The effect of the biofilm system on nitrogen and chromium removal was characterized by measuring the changes in the quality of influent and effluent water. The pattern of biofilm changes was analyzed by measuring biofilm content and thickness and characterizing extracellular polymer substances (EPS). Further analysis of the biofilm microbiota characteristics and potential functions revealed the mechanism of strain YC-34 biofortified biofilm. The results revealed that the biofilm system formed could achieve 90.56% nitrate-nitrogen removal with an average initial nitrate-nitrogen concentration of 51.9 mg/L and 40% chromium removal with an average initial hexavalent chromium Cr(VI) concentration of 7.12 mg/L. The biofilm properties of the system were comparatively analyzed during the biofilm formation period, the fluctuation period of Cr(VI)-stressed water quality, and the stabilization period of Cr(VI)-stressed water quality. The biofilm system may be able to increase the structure of hydrogen bonds, the type of protein secondary structure, and the abundance of amino acid-like components in the EPS, which may confer biofilm tolerance to Cr(VI) stress and allow the system to maintain a stable biofilm structure. Furthermore, microbial characterization indicated an increase in microbial diversity in the face of chromium stress, with an increase in the abundance of nitrogen removal-associated functional microbiota and an increasing trend in the abundance of nitrogen transfer pathways. These results demonstrate that the biofilm system is stable in nitrogen and chromium removal. This bioaugmentation method may provide a new way for the remediation of heavy metal-polluted water bodies and also provides theoretical and application parameters for the popularization and application of biofilm systems.
Topics: Nitrates; Denitrification; Nitrogen; Chromium; Biofilms; Bacteria
PubMed: 38412631
DOI: 10.1016/j.ecoenv.2024.116156 -
Journal of Ophthalmic Inflammation and... Feb 2024To describe a puzzling case of endophthalmitis caused by three unusual bacteria after intravitreal injection, its outcome, and underlying questions.
PURPOSE
To describe a puzzling case of endophthalmitis caused by three unusual bacteria after intravitreal injection, its outcome, and underlying questions.
FINDINGS
A 70-year-old female patient was diagnosed with acute endophthalmitis following intravitreal aflibercept injection for age-related macular degeneration. A standard tap and inject procedure was performed. Microbiological analyses on the anterior chamber and vitreous samples yielded the presence of three non-fermenting Gram-negative rods: Pseudomonas stutzeri, Stenotrophomonas maltophilia, and Ochrobactrum anthropi. The outcome was favorable after intravitreal injections of vancomycin and ceftazidime, with an almost complete recovery of the visual acuity to its baseline level. No potential source of infection was identified.
CONCLUSION
Endophthalmitis following intravitreal injection can be caused by a wide variety of bacteria, including some rare Gram-negative species. They can sometimes co-exist in a single patient, but their virulence may vary greatly. Due to the variable antibiotic susceptibility and frequent multiresistance associated with non-fermenting Gram-negative rods, a prompt microbiological approach is required. Favorable outcome can be achieved with standard management.
PubMed: 38334879
DOI: 10.1186/s12348-023-00376-9 -
Journal of Inorganic Biochemistry Apr 2024Cytochrome c (c) is a diheme protein implicated as an electron donor to cbb oxidases in multiple pathogenic bacteria. Despite its prevalence, understanding of how...
Cytochrome c (c) is a diheme protein implicated as an electron donor to cbb oxidases in multiple pathogenic bacteria. Despite its prevalence, understanding of how specific structural features of c optimize its function is lacking. The human pathogen Neisseria gonorrhoeae (Ng) thrives in low oxygen environments owing to the activity of its cbb oxidase. Herein, we report characterization of Ng c. Spectroelectrochemistry experiments of the wild-type (WT) protein have shown that the two Met/His-ligated hemes differ in potentials by ∼100 mV, and studies of the two His/His-ligated variants provided unambiguous assignment of heme A from the N-terminal domain of the protein as the high-potential heme. The crystal structure of the WT protein at 2.45 Å resolution has revealed that the two hemes differ in their solvent accessibility. In particular, interactions made by residues His57 and Ser59 in Loop1 near the axial ligand Met63 contribute to the tight enclosure of heme A, working together with the surface charge, to raise the reduction potential of the heme iron in this domain. The structure reveals a prominent positively-charged patch, which encompasses surfaces of both domains. In contrast to prior findings with c from Pseudomonas stutzeri, the interdomain interface of Ng c contributes minimally to the values of the heme iron potentials in the two domains. Analyses of the heme solvent accessibility, interface properties, and surface charges offer insights into the interplay of these structural elements in tuning redox properties of c and other multiheme proteins.
Topics: Humans; Neisseria gonorrhoeae; Oxidation-Reduction; Cytochromes c; Oxidoreductases; Heme; Iron; Solvents
PubMed: 38330683
DOI: 10.1016/j.jinorgbio.2024.112496 -
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 -
Journal of Advanced Research Dec 2023Transcription of biological nitrogen fixation (nif) genes is activated by the NifA protein which recognizes specific activating sequences upstream of σ-dependent nif...
INTRODUCTION
Transcription of biological nitrogen fixation (nif) genes is activated by the NifA protein which recognizes specific activating sequences upstream of σ-dependent nif promoters. The large quantities of nitrogenase which can make up 20% of the total proteins in the cell indicates high transcription activating efficiency of NifA and high transcription level of nifHDK nitrogenase genes.
OBJECTIVES
Development of an efficient gene transcription activating strategy in bacteria based on positive transcription regulatory proteins and their regulating DNA sequences.
METHODS
We designed a highly efficient gene transcription activating strategy in which the nifA gene was placed directly downstream of its regulating sequences. The NifA protein binds its regulating sequences and stimulates transcription of itself and downstream genes. Overexpressed NifA causes transcription activation by positive reinforcement.
RESULTS
When this gene transcription activating strategy was used to overexpress NifA in Pseudomonas stutzeri DSM4166 containing the nif gene cluster, the nitrogenase activity was increased by 368 folds which was 16 times higher than that obtained by nifA driven by the strongest endogenous constitutive promoter. When this strategy was used to activate transcription of exogenous biosynthetic genes for the plant auxin indole-3-acetic acid and the antitumor alkaloid pigment prodigiosin in DSM4166, both of them resulted in better performance than the strongest endogenous constitutive promoter and the highest reported productions in heterologous hosts to date. Finally, we demonstrated the universality of this strategy using the positive transcriptional regulator of the psp operon, PspF, in E. coli and the pathway-specific positive transcription regulator of the polyene antibiotic salinomycin biosynthesis, SlnR, in Streptomyces albus.
CONCLUSION
Many positive transcription regulatory proteins and their regulating DNA sequences have been identified in bacteria. The gene transcription activating strategy developed in this study will have broad applications in molecular biology and biotechnology.
PubMed: 38123018
DOI: 10.1016/j.jare.2023.12.015