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Frontiers in Bioengineering and... 2024In this study, native ureolytic bacteria were isolated from copper tailings soils to perform microbial-induced carbonate precipitation (MICP) tests and evaluate their...
In this study, native ureolytic bacteria were isolated from copper tailings soils to perform microbial-induced carbonate precipitation (MICP) tests and evaluate their potential for biocement formation and their contribution to reduce the dispersion of particulate matter into the environment from tailings containing potentially toxic elements. It was possible to isolate a total of 46 bacteria; among them only three showed ureolytic activity: T130-1, sp. T130-13 and sp. T130-14. Biocement cores were made by mixing tailings with the isolated bacteria in presence of urea, resulting similar to those obtained with and used as positive control. Indeed, XRD analysis conducted on biocement showed the presence of microcline ( 17%; 11. 9%), clinochlore (, 6.9%) and magnesiumhornblende ( sp. 17.8%; 14.6%); all these compounds were not initially present in the tailings soils. Moreover the presence of calcite (control 0.828%; sp. 5.4%) and hematite (control 0.989%; 6.4%) was also significant unlike the untreated control. The development of biofilms containing abundant amount of Ca, C, and O on microscopic soil particles was evidenced by means of FE-SEM-EDX and XRD. Wind tunnel tests were carried out to investigate the resistance of biocement samples, accounted for a mass loss five holds lower than the control, i.e., the rate of wind erosion in the control corresponded to 82 g/mh while for the biocement treated with sp. it corresponded to only 16.371 g/mh. Finally, in compression tests, the biocement samples prepared with (28.578 psi) and sp. (28.404 psi) showed values similar to those obtained with (27.102 psi), but significantly higher if compared to the control (15.427 psi), thus improving the compression resistance capacity of the samples by 85.2% and 84.1% with respect to the control. According to the results obtained, the biocement samples generated with the native strains showed improvements in the mechanical properties of the soil supporting them as potential candidates in applications for the stabilization of mining liabilities in open environments using bioaugmentation strategies with native strains isolated from the same mine tailing.
PubMed: 38938979
DOI: 10.3389/fbioe.2024.1393334 -
BMC Microbiology Jun 2024Bacterial antimicrobial resistance poses a severe threat to humanity, necessitating the urgent development of new antibiotics. Recent advances in genome sequencing offer...
BACKGROUND
Bacterial antimicrobial resistance poses a severe threat to humanity, necessitating the urgent development of new antibiotics. Recent advances in genome sequencing offer new avenues for antibiotic discovery. Paenibacillus genomes encompass a considerable array of antibiotic biosynthetic gene clusters (BGCs), rendering these species as good candidates for genome-driven novel antibiotic exploration. Nevertheless, BGCs within Paenibacillus genomes have not been extensively studied.
RESULTS
We conducted an analysis of 554 Paenibacillus genome sequences, sourced from the National Center for Biotechnology Information database, with a focused investigation involving 89 of these genomes via antiSMASH. Our analysis unearthed a total of 848 BGCs, of which 716 (84.4%) were classified as unknown. From the initial pool of 554 Paenibacillus strains, we selected 26 available in culture collections for an in-depth evaluation. Genomic scrutiny of these selected strains unveiled 255 BGCs, encoding non-ribosomal peptide synthetases, polyketide synthases, and bacteriocins, with 221 (86.7%) classified as unknown. Among these strains, 20 exhibited antimicrobial activity against the gram-positive bacterium Micrococcus luteus, yet only six strains displayed activity against the gram-negative bacterium Escherichia coli. We proceeded to focus on Paenibacillus brasilensis, which featured five new BGCs for further investigation. To facilitate detailed characterization, we constructed a mutant in which a single BGC encoding a novel antibiotic was activated while simultaneously inactivating multiple BGCs using a cytosine base editor (CBE). The novel antibiotic was found to be localized to the cell wall and demonstrated activity against both gram-positive bacteria and fungi. The chemical structure of the new antibiotic was elucidated on the basis of ESIMS, 1D and 2D NMR spectroscopic data. The novel compound, with a molecular weight of 926, was named bracidin.
CONCLUSIONS
This study outcome highlights the potential of Paenibacillus species as valuable sources for novel antibiotics. In addition, CBE-mediated dereplication of antibiotics proved to be a rapid and efficient method for characterizing novel antibiotics from Paenibacillus species, suggesting that it will greatly accelerate the genome-based development of new antibiotics.
Topics: Paenibacillus; Anti-Bacterial Agents; Multigene Family; Genome, Bacterial; Peptide Synthases; Polyketide Synthases; Bacteriocins; Biosynthetic Pathways; Bacterial Proteins; Drug Discovery
PubMed: 38937695
DOI: 10.1186/s12866-024-03375-5 -
Microorganisms May 2024Hot springs worldwide can be a source of extremophilic microorganisms of biotechnological interest. In this study, samplings of a hot spring in Hidalgo, Mexico, were...
Hot springs worldwide can be a source of extremophilic microorganisms of biotechnological interest. In this study, samplings of a hot spring in Hidalgo, Mexico, were conducted to isolate, identify, and characterize morphologically, biochemically, and molecularly those bacterial strains with potential industrial applications. In addition, a physicochemical and geochemical examination of the hot spring was conducted to fully understand the study region and its potential connection to the strains discovered. The hot spring was classified as sulfate-calcic according to the Piper Diagram; the hydrogeochemical analysis showed the possible interactions between minerals and water. Eighteen bacterial strains were isolated with optimal growth temperatures from 50 to 55 °C. All strains are Gram-positive, the majority having a rod shape, and one a round shape, and 17 produce endospores. Hydrolysis tests on cellulose, pectin, and xylan agar plates demonstrated enzymatic activity in some of the strains. Molecular identification through the 16S rDNA gene allowed classification of 17 strains within the Phylum Firmicutes and one within Deinococcus-Thermus. The bacterial strains were associated with the genera , , , , and , indicating a diversity of bacterial strains with potential industrial applications.
PubMed: 38930448
DOI: 10.3390/microorganisms12061066 -
Plants (Basel, Switzerland) May 2024Enhancing the aerobic stability of whole-plant corn silage is essential for producing high-quality silage. Our research assessed the effect of inoculation with or and...
Enhancing the aerobic stability of whole-plant corn silage is essential for producing high-quality silage. Our research assessed the effect of inoculation with or and its modulation of the bacterial and fungal microbial community structure in an aerobic stage of whole-plant corn silage. Following treatment with a distilled sterile water control, , and (2 × 10 cfu/g), whole-plant corn was ensiled for 60 days. Samples were taken on days 0, 3, and 7 of aerobic exposure, and the results showed that inoculation with or improved the aerobic stability of silage when compared to the effect of the control ( < 0.05). Inoculation with attenuated the increase in pH value and the decrease in lactic acid in the aerobic stage ( < 0.05), reducing the filamentous fungal counts. On the other hand, inoculation with or increased the diversity of the fungal communities ( < 0.05), complicating the correlation between bacteria or fungi, reducing the relative abundance of and in bacterial communities, and inhibiting the tendency of to replace in fungal communities, thus delaying the aerobic spoilage process. Due to the prevention of the development of aerobic spoilage microorganisms, the silage injected with or exhibited improved aerobic stability.
PubMed: 38891280
DOI: 10.3390/plants13111471 -
International Journal of Food... Jun 2024The Protected Designation of Origin (PDO) indication for foods intends to guarantee the conditions of production and the geographical origin of regional products within...
The Protected Designation of Origin (PDO) indication for foods intends to guarantee the conditions of production and the geographical origin of regional products within the European Union. Honey products are widely consumed due to their health-promoting properties and there is a general interest in tracing their authenticity. In this regard, metagenomics sequencing and machine learning (ML) have been proposed as complementary technologies to improve the traceability methods of foods. Therefore, the aim of this study was to analyze the metagenomic profiles of Spanish honeys from three different PDOs (Granada, Tenerife and Villuercas-Ibores), and compare them with non-PDO honeys using ML models (PLS, RF, LOGITBOOST, and NNET). According to the results obtained, non-PDO honeys and Granada PDO showed higher beta diversity values than Tenerife and Villuercas-Ibores PDOs. ML classification of honey products allowed the identification of different microbial biomarkers of the geographical origin of honeys: Lactobacillus kunkeei, Parasaccharibacter apium and Lactobacillus helsingborgensis for PDO honeys and Paenibacillus larvae, Lactobacillus apinorum and Klebsiella pneumoniae for non-PDO honeys. In addition, potential microbial biomarkers of some honey varieties including L. kunkeei for Albaida and Retama del Teide varieties, and P. apium for Tajinaste variety, were identified. ML models were validated on an independent set of samples leading to high accuracy rates (above 90 %). This work demonstrates the potential of ML to differentiate different types of honey using metagenome-based methods, leading to high performance metrics. In addition, ML models discriminate both the geographical origin and variety of products corresponding to different PDOs and non-PDO products. Results here presented may contribute to develop enhanced traceability and authenticity methods that could be applied to a wide range of foods.
PubMed: 38879955
DOI: 10.1016/j.ijfoodmicro.2024.110789 -
Proceedings of the National Academy of... Jun 2024
PubMed: 38870063
DOI: 10.1073/pnas.2410191121 -
Microbial Cell Factories Jun 2024The gram-positive bacterium Bacillus subtilis is widely used for industrial enzyme production. Its ability to secrete a wide range of enzymes into the extracellular...
BACKGROUND
The gram-positive bacterium Bacillus subtilis is widely used for industrial enzyme production. Its ability to secrete a wide range of enzymes into the extracellular medium especially facilitates downstream processing since cell disruption is avoided. Although various heterologous enzymes have been successfully secreted with B. subtilis, the secretion of cytoplasmic enzymes with high molecular weight is challenging. Only a few studies report on the secretion of cytoplasmic enzymes with a molecular weight > 100 kDa.
RESULTS
In this study, the cytoplasmic and 120 kDa β-galactosidase of Paenibacillus wynnii (β-gal-Pw) was expressed and secreted with B. subtilis SCK6. Different strategies were focused on to identify the best secretion conditions. Tailormade codon-optimization of the β-gal-Pw gene led to an increase in extracellular β-gal-Pw production. Consequently, the optimized gene was used to test four signal peptides and two promoters in different combinations. Differences in extracellular β-gal-Pw activity between the recombinant B. subtilis strains were observed with the successful secretion being highly dependent on the specific combination of promoter and signal peptide used. Interestingly, signal peptides of both the general secretory- and the twin-arginine translocation pathway mediated secretion. The highest extracellular activity of 55.2 ± 6 µkat/L was reached when secretion was mediated by the PhoD signal peptide and expression was controlled by the P promoter. Production of extracellular β-gal-Pw was further enhanced 1.4-fold in a bioreactor cultivation to 77.5 ± 10 µkat/L with secretion efficiencies of more than 80%.
CONCLUSION
For the first time, the β-gal-Pw was efficiently secreted with B. subtilis SCK6, demonstrating the potential of this strain for secretory production of cytoplasmic, high molecular weight enzymes.
Topics: Bacillus subtilis; beta-Galactosidase; Paenibacillus; Molecular Weight; Cytoplasm; Promoter Regions, Genetic; Bacterial Proteins; Recombinant Proteins; Protein Sorting Signals
PubMed: 38867249
DOI: 10.1186/s12934-024-02445-7 -
Microbiology Resource Announcements Jun 2024In this study, we have identified and characterized three genomes from bacteria isolated from the rhizosphere of CMAA1738 and CMAA1739 were obtained from the wheat...
In this study, we have identified and characterized three genomes from bacteria isolated from the rhizosphere of CMAA1738 and CMAA1739 were obtained from the wheat landrace Iran 1-29-11334, and CMAA1741 was isolated from the wheat landrace Karakilcik.
PubMed: 38860798
DOI: 10.1128/mra.00036-24 -
International Journal of Systematic and... Jun 2024
Topics: Bees; Animals; Paenibacillus; RNA, Ribosomal, 16S; DNA, Bacterial; Phylogeny; Sequence Analysis, DNA; Bacterial Typing Techniques; Fatty Acids; Base Composition
PubMed: 38848114
DOI: 10.1099/ijsem.0.006408 -
Microbiology Resource Announcements Jun 2024sp. RC80 was isolated from temperate deciduous forest soil in New England. The assembled genome is a single contig with 5,977,337 bp and 97.15% estimated completion....
sp. RC80 was isolated from temperate deciduous forest soil in New England. The assembled genome is a single contig with 5,977,337 bp and 97.15% estimated completion. RC80 contains features for 2,3-butanediol dehydrogenase production and pathways involved in ethanol production.
PubMed: 38847544
DOI: 10.1128/mra.01067-23