-
The ISME Journal Mar 2022Trophic interactions play a central role in driving microbial community assembly and function. In gut or soil ecosystems, successful inoculants are always facilitated by...
Trophic interactions play a central role in driving microbial community assembly and function. In gut or soil ecosystems, successful inoculants are always facilitated by efficient colonization; however, the metabolite exchanges between inoculants and resident bacteria are rarely studied, particularly in the rhizosphere. Here, we used bioinformatic, genetic, transcriptomic, and metabonomic analyses to uncover syntrophic cooperation between inoculant (Bacillus velezensis SQR9) and plant-beneficial indigenous Pseudomonas stutzeri in the cucumber rhizosphere. We found that the synergistic interaction of these two species is highly environmental dependent, the emergence of syntrophic cooperation was only evident in a static nutrient-rich niche, such as pellicle biofilm in addition to the rhizosphere. Our results identified branched-chain amino acids (BCAAs) biosynthesis pathways are involved in syntrophic cooperation. Genome-scale metabolic modeling and metabolic profiling also demonstrated metabolic facilitation among the bacterial strains. In addition, biofilm matrix components from Bacillus were essential for the interaction. Importantly, the two-species consortium promoted plant growth and helped plants alleviate salt stress. In summary, we propose a mechanism in which synergic interactions between a biocontrol bacterium and a partner species promote plant health.
Topics: Bacillus; Microbiota; Plant Roots; Pseudomonas stutzeri; Rhizosphere; Soil Microbiology
PubMed: 34593997
DOI: 10.1038/s41396-021-01125-3 -
Frontiers in Microbiology 2022Soil salinity is one of the most important abiotic factors limiting plant productivity. The aim of this study was to determine the effect of selected halotolerant plant...
Soil salinity is one of the most important abiotic factors limiting plant productivity. The aim of this study was to determine the effect of selected halotolerant plant growth-promoting endophytes (PGPEs, ISE12 and CSE9) on the growth parameters of barley (), lettuce (), and sunflower () cultivated under salt stress conditions. A negative effect of two higher tested salinities (150 and 300 mM NaCl) was observed on the growth parameters of all investigated plants, including germination percentage and index (decreasing compared to the non-saline control variant in the ranges 5.3-91.7 and 13.6-90.9%, respectively), number of leaves (2.2-39.2%), fresh weight (24.2-81.6%); however, differences in salt stress tolerance among the investigated crops were observed ( > > ). Our data showed that the most crucial traits affected by endophyte inoculation under salt stress were chlorophyll concentration, leaf development, water storage, root development, and biomass accumulation. Thus, the influence of endophytes was species specific. CSE9 promoted the growth of all tested plant species and could be considered a universal PGPEs for many plant genotypes cultivated under saline conditions (e.g., increasing of fresh weight compared to the non-inoculated control variant of barley, lettuce, and sunflower in the ranges 11.4-246.8, 118.9-201.2, and 16.4-77.7%, respectively). ISE12 stimulated growth and mitigated salinity stress only in the case of barley. Bioaugmentation of crops with halotolerant bacterial strains can alleviate salt stress and promote plant growth; however, the selection of compatible strains and the verification of universal plant stress indicators are the key factors.
PubMed: 35350624
DOI: 10.3389/fmicb.2022.788893 -
Analytical Chemistry Aug 2023Small proteins of around 50 aa in length have been largely overlooked in genetic and biochemical assays due to the inherent challenges with detecting and characterizing...
Small proteins of around 50 aa in length have been largely overlooked in genetic and biochemical assays due to the inherent challenges with detecting and characterizing them. Recent discoveries of their critical roles in many biological processes have led to an increased recognition of the importance of small proteins for basic research and as potential new drug targets. One example is CcoM, a 36 aa subunit of the -type oxidase that plays an essential role in adaptation to oxygen-limited conditions in , a model for the clinically relevant, opportunistic pathogen . However, as no comprehensive data were available in , we devised an integrated, generic approach to study small proteins more systematically. Using the first complete genome as basis, we conducted bottom-up proteomics analyses and established a digest-free, direct-sequencing proteomics approach to study cells grown under aerobic and oxygen-limiting conditions. Finally, we also applied a proteogenomics pipeline to identify missed protein-coding genes. Overall, we identified 2921 known and 29 novel proteins, many of which were differentially regulated. Among 176 small proteins 16 were novel. Direct sequencing, featuring a specialized precursor acquisition scheme, exhibited advantages in the detection of small proteins with higher (up to 100%) sequence coverage and more spectral counts, including sequences with high proline content. Three novel small proteins, uniquely identified by direct sequencing and not conserved beyond , were predicted to form an operon with a conserved protein and may represent genes. These data demonstrate the power of this combined approach to study small proteins in and show its potential for other prokaryotes.
Topics: Pseudomonas stutzeri; Proteomics; Proteogenomics; Pseudomonas aeruginosa; Oxygen
PubMed: 37535005
DOI: 10.1021/acs.analchem.3c00676 -
Infectious Disease Reports Dec 2020bacteria are widespread pathogens that account for considerable infections with significant morbidity and mortality, especially in hospitalized patients. The genus... (Review)
Review
bacteria are widespread pathogens that account for considerable infections with significant morbidity and mortality, especially in hospitalized patients. The genus contains a large number of species; however, the majority of infections are caused by , infections by other species are less reported. is a ubiquitous Gram-negative bacterium that has been reported as a causative agent of some infections, particularly in immunocompromised patients but has rarely been reported as a cause of infective endocarditis. Here, we report a case of a 55-year-old female with no significant medical history who presented with exertional dyspnea, productive cough, and fever. She was diagnosed as a case of acute anterior ST myocardial infarction, underwent double valve replacement surgery, and was found to have infective endocarditis caused by .
PubMed: 33276629
DOI: 10.3390/idr12030020 -
Frontiers in Microbiology 2021is a species complex with extremely broad phenotypic and genotypic diversity. However, very little is known about its diversity, taxonomy and phylogeny at the genomic...
is a species complex with extremely broad phenotypic and genotypic diversity. However, very little is known about its diversity, taxonomy and phylogeny at the genomic scale. To address these issues, we systematically and comprehensively defined the taxonomy and nomenclature for this species complex and explored its genetic diversity using hundreds of sequenced genomes. By combining average nucleotide identity (ANI) evaluation and phylogenetic inference approaches, we identified 123 complex genomes covering at least six well-defined species among all sequenced genomes; of these, 25 genomes represented novel members of this species complex. ANI values of ≥∼95% and digital DNA-DNA hybridization (dDDH) values of ≥∼60% in combination with phylogenomic analysis consistently and robustly supported the division of these strains into 27 genomovars (most likely species to some extent), comprising 16 known and 11 unknown genomovars. We revealed that 12 strains had mistaken taxonomic assignments, while 16 strains without species names can be assigned to the species level within the species complex. We observed an open pan-genome of the complex comprising 13,261 gene families, among which approximately 45% gene families do not match any sequence present in the COG database, and a large proportion of accessory genes. The genome contents experienced extensive genetic gain and loss events, which may be one of the major mechanisms driving diversification within this species complex. Surprisingly, we found that the ectoine biosynthesis gene cluster () was present in all genomes of species complex strains but distributed at very low frequency (43 out of 9548) in other genomes, suggesting a possible origin of the ancestors of species complex in high-osmolarity environments. Collectively, our study highlights the potential of using whole-genome sequences to re-evaluate the current definition of the complex, shedding new light on its genomic diversity and evolutionary history.
PubMed: 35095786
DOI: 10.3389/fmicb.2021.755874 -
Revista Chilena de Infectologia :... Aug 2020
Topics: Pseudomonas stutzeri
PubMed: 33399664
DOI: 10.4067/S0716-10182020000400443 -
Microbiology and Molecular Biology... Jun 2006Pseudomonas stutzeri is a nonfluorescent denitrifying bacterium widely distributed in the environment, and it has also been isolated as an opportunistic pathogen from... (Review)
Review
Pseudomonas stutzeri is a nonfluorescent denitrifying bacterium widely distributed in the environment, and it has also been isolated as an opportunistic pathogen from humans. Over the past 15 years, much progress has been made in elucidating the taxonomy of this diverse taxonomical group, demonstrating the clonality of its populations. The species has received much attention because of its particular metabolic properties: it has been proposed as a model organism for denitrification studies; many strains have natural transformation properties, making it relevant for study of the transfer of genes in the environment; several strains are able to fix dinitrogen; and others participate in the degradation of pollutants or interact with toxic metals. This review considers the history of the discovery, nomenclatural changes, and early studies, together with the relevant biological and ecological properties, of P. stutzeri.
Topics: Biology; Drug Resistance, Bacterial; Ecology; Genes, Bacterial; Genetic Variation; Phylogeny; Pseudomonas stutzeri
PubMed: 16760312
DOI: 10.1128/MMBR.00047-05 -
AMB Express May 2022Psychrotrophic Pseudomonas is one of the significant microbes that lead to putrefaction in chilled meat. One of the biggest problems in the detection of Pseudomonas is...
Psychrotrophic Pseudomonas is one of the significant microbes that lead to putrefaction in chilled meat. One of the biggest problems in the detection of Pseudomonas is that several species are seemingly identical. Currently, antibiotic resistance is one of the most significant challenges facing the world's health and food security. Therefore, this study was designed to apply an accurate technique for eliminating the identification discrepancy of Pseudomonas species and to study their resistance against various antimicrobials. A total of 320 chicken meat specimens were cultivated, and the isolated bacteria' were phenotypically recognized. Protein analysis was carried out for cultured isolates via Microflex LT. The resistance of Pseudomonas isolates was recorded through Vitek® 2 AST-GN83 cards. Overall, 69 samples were identified as Pseudomonas spp. and included 18 Pseudomonas lundensis (P. lundensis), 16 Pseudomonas fragi (P. fragi), 13 Pseudomonas oryzihabitans (P. oryzihabitans), 10 Pseudomonas stutzeri (P. stutzeri), 5 Pseudomonas fluorescens (P. fluorescens), 4 Pseudomonas putida (P. putida), and 3 Pseudomonas aeruginosa (P. aeruginosa) isolates. Microflex LT identified all Pseudomonas isolates (100%) correctly with a score value ≥ 2.00. PCA positively discriminated the identified isolates into various groups. The antimicrobial resistance levels against Pseudomonas isolates were 81.16% for nitrofurantoin, 71% for ampicillin and ampicillin/sulbactam, 65.22% for cefuroxime and ceftriaxone, 55% for aztreonam, and 49.28% for ciprofloxacin. The susceptibilities were 100% for cefotaxime, 98.55% for ceftazidime, 94.20% for each piperacillin/tazobactam and cefepime, 91.3% for cefazolin. In conclusion, chicken meat was found to be contaminated with different Pseudomonas spp., with high incidence rates of P. lundensis. Microflex LT is a potent tool for distinguishing Pseudomonads at the species level.
PubMed: 35532863
DOI: 10.1186/s13568-022-01390-1 -
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 -
Microorganisms Jan 2023Illite is a widely distributed clay mineral with huge reserves in Earth's crust, but its effect on heavy oil biodegradation is rarely reported. This study made an...
Illite is a widely distributed clay mineral with huge reserves in Earth's crust, but its effect on heavy oil biodegradation is rarely reported. This study made an investigation of the interactions between illite and a -heavy oil complex (HO). Results showed that, although illite exerted a negative effect on degrading heavy oil by inhibiting the biodegradation of 64 saturated hydrocarbons (SHs) and 50 aromatic hydrocarbons (AHs), it selectively stimulated the biodegradation of 45 AHs with a specific structure, and its biogenic kaolinization at room temperature (35 °C) and pressure (1 atm) was observed in HO for the first time. The finding points out for the first time that, in HO, illite may change the quasi-sequential of AHs biodegradation of heavy oil, as well as its kaolinization without clay intermediate.
PubMed: 36838295
DOI: 10.3390/microorganisms11020330