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Microorganisms Jun 2023AZO16M2, was characterized for its phosphate solubilization capacity to improve the establishment and survival of var. Valery seedlings under ex-acclimation. Three...
AZO16M2, was characterized for its phosphate solubilization capacity to improve the establishment and survival of var. Valery seedlings under ex-acclimation. Three phosphorus sources (Rock Phosphate (RF), Ca(PO) and KHPO) and two types of substrate (sand:vermiculite (1:1) and Premix N°8) were selected. The factorial analysis of variance ( < 0.05) showed that AZO16M2 (OQ256130) solubilizes Ca(PO) in solid medium, with a Solubilization Index (SI) of 3.77 at 28 °C (pH 6.8). In liquid medium, it was observed that produced 29.6 mg/L soluble P (pH 4.4), and synthesized organic acids (oxalic, D-gluconic, 2-ketogluconic and malic), Indole Acetic Acid (IAA) (33.90 ppm) and siderophores (+). Additionally, acid and alkaline phosphatases (2.59 and 2.56 µg pNP/mL/min) were detected. The presence of the pyrroloquinoline-quinone (PQQ) cofactor gene was confirmed. After inoculating AZO16M2 to in sand:vermiculite with RF, the chlorophyll content was 42.38 SPAD (Soil Plant Analysis Development). Aerial fresh weight (AFW), aerial dry weight (ADW) and root dry weight (RDW) were superior to the control by 64.15%, 60.53% and 43.48%, respectively. In Premix N°8 with RF and , 8.91% longer roots were obtained, with 35.58% and 18.76% more AFW and RFW compared with the control as well as 94.45 SPAD. With Ca(PO), values exceeded the control by 14.15% RFW, with 45.45 SPAD. AZO16M2 favored the ex-climatization of through improving seedling establishment and survival.
PubMed: 37375098
DOI: 10.3390/microorganisms11061596 -
BMC Genomics Mar 2024Rahnella perminowiae S11P1 and Variovorax sp. S12S4 are two plant growth-promoting rhizobacteria that were previously isolated from the rhizosphere of Crocus sativus L....
Functional analysis and comparative genomics of Rahnella perminowiae S11P1 and Variovorax sp. S12S4, two plant growth-promoting rhizobacteria isolated from Crocus sativus L. (saffron) rhizosphere.
BACKGROUND
Rahnella perminowiae S11P1 and Variovorax sp. S12S4 are two plant growth-promoting rhizobacteria that were previously isolated from the rhizosphere of Crocus sativus L. (saffron), and have demonstrated interesting PGP activities and promising results when used as inoculants in field trials. To further elucidate the molecular mechanisms underlying their beneficial effects on plant growth, comprehensive genome mining of S11P1 and S12S4 and comparative genomic analysis with closely related strains were conducted.
RESULTS
Functional annotation of the two strains predicted a large number of genes involved in auxin and siderophore production, nitrogen fixation, sulfur metabolism, organic acid biosynthesis, pyrroloquinoline quinone production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, volatile organic compounds production, and polyamine biosynthesis. In addition, numerous genes implicated in plant-bacteria interactions, such as those involved in chemotaxis and quorum sensing, were predicted. Moreover, the two strains carried genes involved in bacterial fitness under abiotic stress conditions. Comparative genomic analysis revealed an open pan-genomic structure for the two strains. COG annotation showed that higher fractions of core and accessory genes were involved in the metabolism and transport of carbohydrates and amino acids, suggesting the metabolic versatility of the two strains as effective rhizosphere colonizers. Furthermore, this study reports the first comparison of Multilocus sequence analysis (MLSA) and core-based phylogenies of the Rahnella and Variovorax genera.
CONCLUSIONS
The present study unveils the molecular mechanisms underlying plant growth promotion and biocontrol activity of S11P1 and S12S4, and provides a basis for their further biotechnological application in agriculture.
Topics: Crocus; Rahnella; Rhizosphere; Plant Development; Bacteria; Genomics; Alphaproteobacteria; Plant Roots; Soil Microbiology
PubMed: 38500021
DOI: 10.1186/s12864-024-10088-6 -
Scientific Reports Jul 2023Persian walnut (Juglans regia) has a considerable economic importance worldwide. However, the vigor and vitality of walnut trees were heavily affected by bark canker...
Persian walnut (Juglans regia) has a considerable economic importance worldwide. However, the vigor and vitality of walnut trees were heavily affected by bark canker during the last few years. Irregular longitudinal cankers in the outer bark, stem tissue necrosis, and bleeding with black-colored exudates walnut trees were observed in Kermanshah, Hamedan, Markazi, Alborz, Isfahan, Qom, Semnan, and Razavi Khorasan provinces in western, central and eastern Iran during 2018 and 2019. A total of 150 symptomatic samples were collected from affected walnut trees in order to identify bacteria associated with walnut decline. Two-hundred sixty strains with a metallic green sheen were isolated on EMB-agar medium. The pathogenicity of all strains was proved by inoculating a suspension of the bacterial strains under the bark of immature walnut fruits cv. 'Hartley'. Ninety-five strains caused necrosis and a dark-colored region in the mesocarp around the inoculation site 14 days post-inoculation. Moreover, 12 representative strains induced necrotic and black-colored tissues in the bark of young green twigs of two-year old walnut seedling cv. 'Chandler'. The strains were classified into four categories based on conventional phenotypic characters confirmed with the 16S rRNA gene sequences. A phylogenetic tree based on the concatenated sequences of two housekeeping gene fragments, gyrB and infB, indicated that strains including I1, Q6, and S6 were grouped in a cluster with Gibbsiella quercinecans FBR97 as well as strains I2, I5, and KE6 were clustered with Rahnella victoriana FRB 225. Moreover, strains MR1, MR3, and MR5 were grouped with the Enterobacter hormaechei subsp. hoffmannii DSM 14563. The phylogenetic analyses based on the partial sequencing of housekeeping genes including fusA, pyrG, and leuS revealed that strains KH1, KH3, and KH7 belong to Citrobacter braakii species. To the best of our knowledge, this is the first report of C. braakii and E. hormaechei as plant pathogens and R. victoriana associated with walnut decline.
Topics: Juglans; Phylogeny; RNA, Ribosomal, 16S; Necrosis
PubMed: 37438442
DOI: 10.1038/s41598-023-38427-9 -
Multi-omics analysis of miRNA-mediated intestinal microflora changes in crucian carp infected with .Frontiers in Immunology 2024Infection by an emerging bacterial pathogen caused enteritis and septicemia in fish. However, the molecular pathogenesis of enteritis induced by infection and its...
Infection by an emerging bacterial pathogen caused enteritis and septicemia in fish. However, the molecular pathogenesis of enteritis induced by infection and its interacting mechanism of the intestinal microflora associated with microRNA (miRNA) immune regulation in crucian carp are still unclear. In this study, intraperitoneally injected with KCL-5 was used as an experimental animal model, and the intestinal pathological changes, microflora, and differentially expressed miRNAs (DEMs) were investigated by multi-omics analysis. The significant changes in histopathological features, apoptotic cells, and enzyme activities (e.g., lysozyme (LYS), alkaline phosphatase (AKP), alanine aminotransferase (ALT), aspartate transaminase (AST), and glutathione peroxidase (GSH-Px)) in the intestine were examined after infection. Diversity and composition analysis of the intestinal microflora clearly demonstrated four dominant bacteria: Proteobacteria, Fusobacteria, Bacteroidetes, and Firmicutes. A total of 87 DEMs were significantly screened, and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the potential target genes were mainly involved in the regulation of lipid, glutathione, cytosine, and purine metabolism, which participated in the local immune response through the intestinal immune network for IgA production, lysosome, and Toll-like receptor (TLR) pathways. Moreover, the expression levels of 11 target genes (e.g., , , , , , , , , , , and ) related to inflammation and immunity were verified by qRT-PCR detection. The correlation analysis indicated that the abundance of intestinal Firmicutes and Proteobacteria was significantly associated with the high local expression of miR-203/, miR-129/, and miR-205/. These findings will help to elucidate the molecular regulation mechanism of the intestinal microflora, inflammation, and immune response-mediated miRNA-target gene axis in cyprinid fish.
Topics: Animals; Goldfish; Carps; Rahnella; NF-kappa B; Multiomics; Gastrointestinal Microbiome; Tumor Necrosis Factor-alpha; Inflammation; Enteritis; Transforming Growth Factor beta; MicroRNAs
PubMed: 38426108
DOI: 10.3389/fimmu.2024.1335602 -
Royal Society Open Science Nov 2023Enterobacterales of clinical importance for humans and domestic animals are now commonly detected among wildlife worldwide. However, few studies have investigated their...
Enterobacterales of clinical importance for humans and domestic animals are now commonly detected among wildlife worldwide. However, few studies have investigated their prevalence among bats, particularly in bat species living near humans. In this study, we assessed the occurrence of Extended-spectrum beta-lactamase-producing (ESBL) and carbapenemase-resistant (CR) Enterobacterales in rectal swabs of bats submitted to the Chilean national rabies surveillance program from 2021 to 2022. From the 307 swabs screened, 47 (15%) harboured cefotaxime-resistant Enterobacterales. Bats carrying these bacteria originated from 9 out of the 14 Chilean regions. Most positive samples were obtained from ( = 42), but also , and . No Enterobacterales were resistant to imipenem. All ESBL-Enterobacterales were confirmed as by MALDI-TOF. No other ESBL or CR Enterobacterales were detected. To our knowledge, this is the first screening of antibiotic-resistant bacteria in wild bats of Chile, showing the bat faecal carriage of naturally resistant to cephalosporins, but also including acquired resistance to important antibiotics for public health such as amoxicillin with clavulanic acid. Our results suggest unknown selective pressures on , but low or no carriage of ESBL or CR and spp. Future studies should assess the zoonotic and environmental implications of , which are likely present in the guano left by bats roosting in human infrastructures.
PubMed: 38026036
DOI: 10.1098/rsos.231177 -
Journal of Dairy Science Mar 2024Ropy defect of pasteurized fluid milk is a type of spoilage which manifests itself by an increased viscosity, slimy body, and string-like flow during pouring. This...
Phenotypic and genomic characterizations of Klebsiella pneumoniae ssp. pneumoniae and Rahnella inusitata strains reveal no clear association between genetic content and ropy phenotype.
Ropy defect of pasteurized fluid milk is a type of spoilage which manifests itself by an increased viscosity, slimy body, and string-like flow during pouring. This defect has, among other causes, been attributed to the growth, proliferation and exopolysaccharide production by coliform bacteria, which are most commonly introduced in milk as post-pasteurization contaminants. As we identified both Klebsiella pneumoniae ssp. pneumoniae and Rahnella inusitata that were linked to a ropy defect, the goal of this study was to characterize 3 K. pneumoniae ssp. pneumoniae strains and 2 R. inusitata for (1) their ability to grow and cause ropy defect in milk at 6°C and 21°C and to (2) probe the genetic basis for observed ropy phenotype. Although all K. pneumoniae ssp. pneumoniae and R. inusitata strains showed net growth of >4 log over 48 h in UHT milk at 21°C, only R. inusitata strains displayed growth during 28-d incubation period at 6°C (>6 log). Two out of 3 K. pneumoniae ssp. pneumoniae strains were capable of causing the ropy defect in milk at 21°C, as supported by an increase in the viscosity of milk and string-like flow during pouring; these 2 strains were originally isolated from raw milk. Only one R. inusitata strains was able to cause the ropy defect in milk; this strain was able to cause the defect at both 6°C and 21°C, and was originally isolated from a pasteurized milk. These findings suggest that the potential of K. pneumoniae ssp. pneumoniae and R. inusitata to cause ropy defect in milk is a strain-dependent characteristic. Comparative genomics provided no definitive answer on genetic basis for the ropy phenotype. However, for K. pneumoniae ssp. pneumoniae, genes rffG, rffH, rfbD, and rfbC involved in biosynthesis and secretion of enterobacterial common antigen (ECA) could only be found in the 2 strains that produced ropy defect, and for R. inusitata a set of 2 glycosyltransferase- and flippase genes involved in nucleotide sugar biosynthesis and export could only be identified in the ropy strain. Although these results provide some initial information for potential markers for strains that can cause ropy milk, the relationship between genetic content and ropiness in milk remains poorly understood and merits further investigation.
Topics: Animals; Klebsiella pneumoniae; Genomics; Klebsiella; Rahnella
PubMed: 37944807
DOI: 10.3168/jds.2023-23922 -
Microbiology Spectrum Jun 2023Plants are no longer considered standalone entities; instead, they harbor a diverse community of plant growth-promoting rhizobacteria (PGPR) that aid them in nutrient...
Comparative Genomics and Physiological Investigations Supported Multifaceted Plant Growth-Promoting Activities in Two Hypericum perforatum L.-Associated Plant Growth-Promoting Rhizobacteria for Microbe-Assisted Cultivation.
Plants are no longer considered standalone entities; instead, they harbor a diverse community of plant growth-promoting rhizobacteria (PGPR) that aid them in nutrient acquisition and can also deliver resilience. Host plants recognize PGPR in a strain-specific manner; therefore, introducing untargeted PGPR might produce unsatisfactory crop yields. Consequently, to develop a microbe-assisted Hypericum perforatum L. cultivation technique, 31 rhizobacteria were isolated from the plant's high-altitude Indian western Himalayan natural habitat and characterized for multiple plant growth-promoting attributes. Among 31 rhizobacterial isolates, 26 produced 0.59 to 85.29 μg mL indole-3-acetic acid and solubilized 15.77 to 71.43 μg mL inorganic phosphate; 21 produced 63.12 to 99.92% siderophore units, and 15 exhibited 103.60 to 1,296.42 nmol α-ketobutyrate mg protein h 1-aminocyclopropane-1-carboxylate deaminase (ACCD) activity. Based on superior plant growth-promoting attributes, eight statistically significant multifarious PGPR were further evaluated for an plant growth-promotion assay under poly greenhouse conditions. Plants treated with Kosakonia cowanii HypNH10 and Rahnella variigena HypNH18 showed, by significant amounts, the highest photosynthetic pigments and performance, eventually leading to the highest biomass accumulation. Comparative genome analysis and comprehensive genome mining unraveled their unique genetic features, such as adaptation to the host plant's immune system and specialized metabolites. Moreover, the strains harbor several functional genes regulating direct and indirect plant growth-promotion mechanisms through nutrient acquisition, phytohormone production, and stress alleviation. In essence, the current study endorsed strains HypNH10 and HypNH18 as cogent candidates for microbe-assisted cultivation by highlighting their exclusive genomic signatures, which suggest their unison, compatibility, and multifaceted beneficial interactions with their host and support the excellent plant growth-promotion performance observed in the greenhouse trial. L. (St. John's wort) herbal preparations are among the top-selling products to treat depression worldwide. A significant portion of the overall supply is sourced through wild collection, prompting a rapid decline in their natural stands. Crop cultivation seems lucrative, although cultivable land and its existing rhizomicrobiome are well suited for traditional crops, and its sudden introduction can create soil microbiome dysbiosis. Also, the conventional plant domestication procedures with increased reliance on agrochemicals can reduce the diversity of the associated rhizomicrobiome and plants' ability to interact with plant growth-promoting microorganisms, leading to unsatisfactory crop production alongside harmful environmental effects. Cultivating with crop-associated beneficial rhizobacteria can reconcile such concerns. Based on a combinatorial , plant growth-promotion assay and prediction of plant growth-promoting traits, here we recommend two -associated PGPR, Kosakonia cowanii HypNH10 and HypNH18, to extrapolate as functional bioinoculants for sustainable cultivation.
Topics: Hypericum; Plant Development; Antineoplastic Agents; Genomics
PubMed: 37199656
DOI: 10.1128/spectrum.00607-23 -
Plants (Basel, Switzerland) Sep 2023Plant growth-promoting microorganisms (PGPM) benefit plant health by enhancing plant nutrient-use efficiency and protecting plants against biotic and abiotic stresses....
Identification and Characterization of Beneficial Soil Microbial Strains for the Formulation of Biofertilizers Based on Native Plant Growth-Promoting Microorganisms Isolated from Northern Mexico.
Plant growth-promoting microorganisms (PGPM) benefit plant health by enhancing plant nutrient-use efficiency and protecting plants against biotic and abiotic stresses. This study aimed to isolate and characterize autochthonous PGPM from important agri-food crops and nonagricultural plants to formulate biofertilizers. Native microorganisms were isolated and evaluated for PGP traits (K, P, and Zn solubilization, N-fixation, NH-, IAA and siderophore production, and antifungal activity against ). Isolates were tested on radish and broccoli seedlings, evaluating 19 individual isolates and 12 microbial consortia. Potential bacteria were identified through DNA sequencing. In total, 798 bacteria and 209 fungi were isolated. Isolates showed higher mineral solubilization activity than other mechanisms; 399 bacteria and 156 fungi presented mineral solubilization. Bacteria were relevant for nitrogen fixation, siderophore, IAA (29-176 mg/L), and ammonia production, while fungi for growth inhibition (40-69%). Twenty-four bacteria and eighteen fungi were selected for their PGP traits. Bacteria had significantly (ANOVA, < 0.05) better effects on plants than fungi; treatments improved plant height (23.06-51.32%), leaf diameter (25.43-82.91%), and fresh weight (54.18-85.45%) in both crops. Most potential species belonged to and genera. This work validated a high-throughput approach to screening hundreds of rhizospheric microorganisms with PGP potential isolated from rhizospheric samples.
PubMed: 37765426
DOI: 10.3390/plants12183262 -
Microorganisms Nov 2023Acute oak decline is a high-impact disease causing necrotic lesions on the trunk, crown thinning and the eventual death of oak. Four bacterial species are associated...
Acute oak decline is a high-impact disease causing necrotic lesions on the trunk, crown thinning and the eventual death of oak. Four bacterial species are associated with the lesions-, , and -although an epi-/endophytic lifestyle has also been suggested for these bacteria. However, little is known about their environmental reservoirs or their pathway to endophytic colonisation. This work aimed to investigate the ability of the four AOD-associated bacterial species to survive for prolonged periods within rhizosphere soil, leaves and acorns in vitro, and to design an appropriate method for their recovery. This method was trialled on field samples related to healthy and symptomatic oaks. The in vitro study showed that the majority of these species could survive for at least six weeks within each sample type. Results from the field samples demonstrated that and appear environmentally widespread, indicating multiple routes of endophytic colonisation might be plausible. and were only identified from acorns from healthy and symptomatic trees, indicating they may be inherited members of the endophytic seed microbiome and, despite their ability to survive outside of the host, their environmental occurrence is limited. Future research should focus on preventative measures targeting the abiotic factors of AOD, how endophytic bacteria shift to a pathogenic cycle and the identification of resilient seed stock that is less susceptible to AOD.
PubMed: 38004800
DOI: 10.3390/microorganisms11112789 -
Environmental Analysis, Health and... Dec 2023The indiscriminate deposition of metal-containing substances into the environment contributes significantly to high concentrations of metals in the soil resulting in...
The indiscriminate deposition of metal-containing substances into the environment contributes significantly to high concentrations of metals in the soil resulting in resistance to metals and consequentially to antibiotics by inherent microbes which may eventually spread to other pathogenic microbes thereby elevating disease burden due to antibiotic resistance. The study aimed at determining the co-occurrence of resistance of bacteria isolated from metal-contaminated soil to heavy metals and subsequently, antibiotics. Metal-tolerant bacteria were randomly isolated from top soils from a battery waste site using the pour plate method. Selected isolates were identified using biochemical tests, then, subjected to elevating supplemented concentrations of different metal salts at 100-500 μg/mL to determine the minimum inhibitory concentration. Isolates tolerant to minimum three metals up to 400 μg/mL were subjected to Sulfamethoxazole-trimethoprim (25 μg), Imipenem (10 μg), Amoxicillin (30 μg), Ciprofloxacin (10 μg) and Tigecycline (15 μg) and observations interpreted using the guiding principle of the Clinical and Laboratory Standards Institute. Metal concentrations in the soils exceeded permissible limits. In total, 16 isolates were selected and identified as Proteus sp. (1), Pseudomonas spp. (5), Enterobacter spp. (2), Klebsiella spp. (2), Escherichia spp. (3), Raoultella spp. (2) and Rahnella sp. (1). Thirteen (81.25 %) of all isolates showed multi-resistance to the metals and seven exhibited multidrug-resistance, with 4 (57.1 %) showing resistance to three different classes of antibiotics and 3 (42.9 %) showed resistance to four antibiotic classes. Heavy metal-tolerant bacteria isolated from this study possess co-selection potentials as they showed resistance to different metals and antibiotics classes which is a concern to public health.
PubMed: 38298043
DOI: 10.5620/eaht.2023024