-
ISME Communications Aug 2022Multi-step substrate consumption pathways can promote microbial biodiversity via cross-feeding. If one cell type preferentially consumes a primary substrate rather than...
Multi-step substrate consumption pathways can promote microbial biodiversity via cross-feeding. If one cell type preferentially consumes a primary substrate rather than the subsequently formed intermediates, then other cell types can specialize in consuming the intermediates. While this mechanism for promoting biodiversity is established, predicting the long-term persistence of such cross-feeding interactions remains challenging. Under what conditions will the interaction (and thus biodiversity) persist or disappear? To address this question, we propagated co-cultures of two isogenic strains of the bacterium Pseudomonas stutzeri. One completely reduces nitrate to nitrogen gas but preferentially reduces nitrate rather than nitrite (referred to as the generalist), while the other only reduces nitrite to nitrogen gas (referred to as the specialist). We found that the two strains coexist via nitrite cross-feeding when grown together, but the initial ratio of specialist-to-generalist (r) determines the long-term dynamics of the co-culture. Co-cultures with large initial rs converge to the same r and persist thereafter. Co-cultures with small initial rs also converge to the same r but then become increasingly dominated by the generalist. The likely cause of these different dynamics is that the initial r determines the initial environment, which in turn determines the initial selection pressures and phenotypes acquired by the generalist. Our results demonstrate that initial community composition controls the long-term dynamics and persistence of a cross-feeding interaction, and is therefore an important factor for community development and for engineering communities to achieve desired outcomes.
PubMed: 37938324
DOI: 10.1038/s43705-022-00160-1 -
Frontiers in Microbiology 2022The impact of high concentrations of heavy metals and the loss of functional microorganisms usually affect the nitrogen removal process in wastewater treatment systems....
The impact of high concentrations of heavy metals and the loss of functional microorganisms usually affect the nitrogen removal process in wastewater treatment systems. In the study, a unique auto-aggregating aerobic denitrifier ( strain YC-34) was isolated with potential applications for Cr(VI) biosorption and reduction. The nitrogen removal efficiency and denitrification pathway of the strain were determined by measuring the concentration changes of inorganic nitrogen during the culture of the strain and amplifying key denitrification functional genes. The changes in auto-aggregation index, hydrophobicity index, and extracellular polymeric substances (EPS) characteristic index were used to evaluate the auto-aggregation capacity of the strain. Further studies on the biosorption ability and mechanism of cadmium in the process of denitrification were carried out. The changes in tolerance and adsorption index of cadmium were measured and the micro-characteristic changes on the cell surface were analyzed. The strain exhibited excellent denitrification ability, achieving 90.58% nitrogen removal efficiency with 54 mg/L nitrate-nitrogen as the initial nitrogen source and no accumulation of ammonia and nitrite-nitrogen. Thirty percentage of the initial nitrate-nitrogen was converted to N, and only a small amount of NO was produced. The successful amplification of the denitrification functional genes, , and , further suggested a complete denitrification pathway from nitrate to nitrogen. Furthermore, the strain showed efficient aggregation capacity, with the auto-aggregation and hydrophobicity indices reaching 78.4 and 75.5%, respectively. A large amount of protein-containing EPS was produced. In addition, the strain effectively removed 48.75, 46.67, 44.53, and 39.84% of Cr(VI) with the initial concentrations of 3, 5, 7, and 10 mg/L, respectively, from the nitrogen-containing synthetic wastewater. It also could reduce Cr(VI) to the less toxic Cr(III). FTIR measurements and characteristic peak deconvolution analysis demonstrated that the strain had a robust hydrogen-bonded structure with strong intermolecular forces under the stress of high Cr(VI) concentrations. The current results confirm that the novel denitrifier can simultaneously remove nitrogen and chromium and has potential applications in advanced wastewater treatment for the removal of multiple pollutants from sewage.
PubMed: 35992714
DOI: 10.3389/fmicb.2022.961815 -
British Journal of Biomedical Science 2022There is a paucity of reports on non- (NAPs) in cystic fibrosis, hence this study wished 1). to examine the diversity/frequency of NAPs in an adult CF population, 2) to...
There is a paucity of reports on non- (NAPs) in cystic fibrosis, hence this study wished 1). to examine the diversity/frequency of NAPs in an adult CF population, 2) to compare/contrast the microbiology and genomics of NAPs to and 3) to propose clinical and laboratory criteria to help determine their clinical significance in CF lung pathology. Microbiological data was examined from 100 adult patients with cystic fibrosis from birth to present (31/12/2021), equating to 2455 patient years. 16S rDNA phylogenetic relatedness of NAPs was determined, as well as bioinformatical comparison of whole genomes of against . Ten species were isolated from this patient cohort during this time period, with three species, i.e., and , accounting for the majority (87.5%) of non- reports. This is the first report of the isolation of and in patients with cystic fibrosis. The mean time to first detection of any non- species was 183 months (15.25 years) [median = 229 months (19.1 years)], with a range from 11 months to 338 months (28.2 years). Several of the NAPs were closely related to . NAPs were isolated infrequently and were transient colonisers of the CF airways, in those patients with CF in which they were isolated. A set of ten clinical and laboratory criteria are proposed to provide key indicators, as to the clinical importance of the non- species isolated.
Topics: Adult; Cystic Fibrosis; Humans; Lung; Phylogeny; Pseudomonas Infections; Pseudomonas aeruginosa
PubMed: 35951661
DOI: 10.3389/bjbs.2022.10468 -
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 -
ELife Jul 2022Root exudates are thought to play an important role in plant-microbial interactions. In return for nutrition, soil bacteria can increase the bioavailability of soil...
Root exudates are thought to play an important role in plant-microbial interactions. In return for nutrition, soil bacteria can increase the bioavailability of soil nutrients. However, root exudates typically decrease in situations such as drought, calling into question the efficacy of solvation and bacteria-dependent mineral uptake in such stress. Here, we tested the hypothesis of exudate-driven microbial priming on saplings grown in forest soil in custom-made rhizotron boxes. A 1-month imposed drought and concomitant inoculations with a mix of and , bacteria species isolated from the forest soil, were applied using factorial design. Direct bacteria counts and visualization by confocal microscopy showed that both bacteria associated with roots. Interestingly, root exudation rates increased 2.3-fold with bacteria under drought, as well as irrigation. Forty-four metabolites in exudates were significantly different in concentration between irrigated and drought trees, including phenolic acid compounds and quinate. When adding these metabolites as carbon and nitrogen sources to bacterial cultures of both bacterial species, eight of nine metabolites stimulated bacterial growth. Importantly, soil phosphorous bioavailability was maintained only in inoculated trees, mitigating drought-induced decrease in leaf phosphorus and iron. Our observations of increased root exudation rate when drought and inoculation regimes were combined support the idea of root recruitment of beneficial bacteria, especially under water stress.
Topics: Bacteria; Droughts; Plant Roots; Rhizosphere; Soil; Soil Microbiology; Trees
PubMed: 35858113
DOI: 10.7554/eLife.79679 -
Frontiers in Microbiology 2022Salinity is one of the most damaging abiotic stresses due to climate change impacts that affect the growth and yield of crops, especially in lowland rice fields and...
Salinity is one of the most damaging abiotic stresses due to climate change impacts that affect the growth and yield of crops, especially in lowland rice fields and coastal areas. This research aimed to isolate potential halotolerant plant growth-promoting rhizobacteria from different rhizo-microbiome and use them as effective bioinoculants to improve rice growth under salinity stress conditions. Bioassay using rice seedlings was performed in a randomized block design consisting of 16 treatments (control and 15 bacterial isolates) with three replications. Results revealed that isolates S, S, and S gave higher shoot height, root length, and plant dry weight compared with control (without isolates). Based on molecular characteristics, isolates S and S were identified as and These isolates were able to promote rice growth under salinity stress conditions as halotolerant plant growth-promoting rhizobacteria. These three potent isolates were found to produce indole-3-acetic acid and nitrogenase.
PubMed: 35770168
DOI: 10.3389/fmicb.2022.905210 -
Scientific Reports Jun 2022In this report, we systematically characterize 32 response regulators (RRs) from a metal tolerant groundwater isolate, Pseudomonas stutzeri RCH2 to assess the impact of...
In this report, we systematically characterize 32 response regulators (RRs) from a metal tolerant groundwater isolate, Pseudomonas stutzeri RCH2 to assess the impact of host-derived post-translational phosphorylation. As observed by distinct shifted bands in a phos-tag gel, 12 of the 24 detected RRs show homogenous mixtures of phosphorylated proteins or heterogenous mixtures of unphosphorylated and phosphorylated proteins. By evaluating the phosphorylation state of CzcR and CopR II under varying assay parameters, we found that changes to pH and exogenous addition of phospho-donors (e.g. acetyl phosphate) have little to no effect on phosphorylation state. By applying protein production conditions that decrease the pool of intracellular acetyl-phosphate in E. coli, we found a reduction in the phosphorylated population of CopR II when magnesium was added to the medium, but observed no change in phosphorylated population when CopR II is expressed in E. coli BL21 (DE3) ∆pta, a mutant with a metabolic disruption to the acetyl-phosphate pathway. Therefore, the specific mechanism of post-translational phosphorylation of RRs in E. coli remains obscure. These findings show the importance of characterizing the phosphorylation state of proteins when heterologously expressed, since their biochemical and physiological properties can be dependent on post-translational modification.
Topics: Escherichia coli; Phosphates; Phosphorylation; Protein Processing, Post-Translational; Proteins; Pseudomonas stutzeri
PubMed: 35725867
DOI: 10.1038/s41598-022-13525-2 -
Indian Journal of Ophthalmology Jun 2022To report clinical features, antibiotic susceptibility profile, management, and outcomes of a cluster outbreak of post-cataract surgery Pseudomonas stutzeri...
PURPOSE
To report clinical features, antibiotic susceptibility profile, management, and outcomes of a cluster outbreak of post-cataract surgery Pseudomonas stutzeri endophthalmitis.
METHODS
This was a hospital-based case series in which 14 patients with acute postoperative endophthalmitis who underwent cataract surgery on the same day were included. Based on severity of presentation, they either underwent pars plana vitrectomy (PPV) with intraocular antibiotics (IOAB) or vitreous tap with IOAB. Vitreous aspirates and environmental surveillance samples were inoculated on culture media and further processed by MALDI-TOF MS for identification and Vitek3 for susceptibility profile.
RESULTS
There were 8 females and 6 males with a mean age of 62.14 ± 8.08 years. Presenting signs included corneal folds (100%), hypopyon (57.1%) and fibrin (50%). Ten patients with mild presentation underwent vitreous tap with IOAB. Four patients with severe presentation underwent PPV with IOAB. Pseudomonas stutzeri was isolated from the vitreous samples and was pan-sensitive. Six eyes required multiple interventions. Favorable outcome was obtained in 12 eyes, one eye developed phthisis, and one patient was lost to follow-up.
CONCLUSION
We report the first ever cluster outbreak of Pseudomonas stutzeri endophthalmitis following phacoemulsification with IOL implantation in a single surgeon setting. Majority of the patients had a mild presentation and responded well to targeted anti-microbial treatment.
Topics: Acute Disease; Aged; Anti-Bacterial Agents; Cataract; Disease Outbreaks; Endophthalmitis; Eye Infections, Bacterial; Female; Humans; Male; Middle Aged; Phacoemulsification; Pseudomonas Infections; Pseudomonas stutzeri
PubMed: 35647987
DOI: 10.4103/ijo.IJO_3096_21 -
Frontiers in Cellular and Infection... 2022The gut microbiota is associated with reproductive disorders in multiple ways. This research investigated possible differences in gut microbiome compositions between...
The gut microbiota is associated with reproductive disorders in multiple ways. This research investigated possible differences in gut microbiome compositions between patients with uterine fibroids (UFs) and healthy control subjects in order to further provide new insight into its etiology. Stool samples were collected from 85 participants, including 42 UF patients (case group) and 43 control subjects (control group). The gut microbiota was examined with 16S rRNA quantitative arrays and bioinformatics analysis. The α-diversity in patients with UFs was significantly lower than that of healthy controls and negatively correlated with the number of tumorigeneses. The microbial composition of the UF patients deviated from the cluster of healthy controls. Stool samples from patients with UFs exhibited significant alterations in terms of multiple bacterial phyla, such as Firmicutes, Proteobacteria, Actinobacteria, and Verrucomicrobia. In differential abundance analysis, some bacteria species were shown to be downregulated (.., , , and ) and upregulated (.., and ). Furthermore, the microbial interactions and networks in UFs exhibited lower connectivity and complexity as well as higher clustering property compared to the controls. Taken together, it is possible that gut microbiota dysbiosis has the potential as a risk factor. This study found that UFs are associated with alterations of the gut microbiome diversity and community network connectivity. It provides a new direction to further explore the host-gut microbiota interplay and to develop management and prevention in UF pathogenesis.
Topics: Dysbiosis; Gastrointestinal Microbiome; Humans; Leiomyoma; RNA, Ribosomal, 16S; Verrucomicrobia
PubMed: 35646718
DOI: 10.3389/fcimb.2022.863594 -
Genes May 2022A1501, a plant-associated diazotrophic bacterium, prefers to conform to a nitrogen-fixing biofilm state under nitrogen-deficient conditions. The extracytoplasmic...
A1501, a plant-associated diazotrophic bacterium, prefers to conform to a nitrogen-fixing biofilm state under nitrogen-deficient conditions. The extracytoplasmic function (ECF) sigma factor AlgU is reported to play key roles in exopolysaccharide (EPS) production and biofilm formation in the genus; however, the function of AlgU in A1501 is still unclear. In this work, we mainly investigated the role of in EPS production, biofilm formation and nitrogenase activity in A1501. The mutant Δ showed a dramatic decrease both in the EPS production and the biofilm formation capabilities. In addition, the biofilm-based nitrogenase activity was reduced by 81.4% in the Δ mutant. The transcriptional level of , a key Psl-like (a major EPS in A1501) synthesis-related gene, was almost completely inhibited in the mutant and was upregulated by 2.8-fold in the -overexpressing strain. A predicted AlgU-binding site was identified in the promoter region of . The DNase I footprinting assays indicated that AlgU could directly bind to the promoter, and β-galactosidase activity analysis further revealed mutations of the AlgU-binding boxes drastically reduced the transcriptional activity of the promoter; moreover, we also demonstrated that AlgU was positively regulated by RpoN at the transcriptional level and negatively regulated by the RNA-binding protein RsmA at the posttranscriptional level. Taken together, these data suggest that AlgU promotes EPS production and nitrogen-fixing biofilm formation by directly activating the transcription of , and the expression of AlgU is controlled by RpoN and RsmA at different regulatory levels.
Topics: Bacterial Proteins; Biofilms; Gene Expression Regulation, Bacterial; Nitrogen; Nitrogenase; Pseudomonas stutzeri; Sigma Factor
PubMed: 35627252
DOI: 10.3390/genes13050867