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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 -
Heliyon Jun 2024Endophytic bacteria, living inside plants, are competent plant colonizers, capable of enhancing immune responses in plants and establishing a symbiotic relationship with... (Review)
Review
Endophytic bacteria, living inside plants, are competent plant colonizers, capable of enhancing immune responses in plants and establishing a symbiotic relationship with them. Endophytic bacteria are able to control phytopathogenic fungi while exhibiting plant growth-promoting activity. Here, we discussed the mechanisms of phytopathogenic fungi control and plant growth-promoting actions discovered in some major groups of beneficial endophytic bacteria such as , and . Most of the studied strains in these genera were isolated from the rhizosphere and soils, and a more extensive study of these endophytic bacteria is needed. It is essential to understand the underlying biocontrol and plant growth-promoting mechanisms and to develop an effective screening approach for selecting potential endophytic bacteria for various applications. We have suggested a screening strategy to identify potentially useful endophytic bacteria based on mechanistic phenomena. The discovery of endophytic bacteria with useful biocontrol and plant growth-promoting characteristics is essential for developing sustainable agriculture.
PubMed: 38841467
DOI: 10.1016/j.heliyon.2024.e31573 -
BioRxiv : the Preprint Server For... May 2024The paenilamicins are a group of hybrid non-ribosomal peptide-polyketide compounds produced by the honey bee pathogen that display activity against Gram-positive...
The paenilamicins are a group of hybrid non-ribosomal peptide-polyketide compounds produced by the honey bee pathogen that display activity against Gram-positive pathogens, such as . While paenilamicins have been shown to inhibit protein synthesis, their mechanism of action has remained unclear. Here, we have determined structures of the paenilamicin PamB2 stalled ribosomes, revealing a unique binding site on the small 30S subunit located between the A- and P-site tRNAs. In addition to providing a precise description of interactions of PamB2 with the ribosome, the structures also rationalize the resistance mechanisms utilized by . We could further demonstrate that PamB2 interferes with the translocation of mRNA and tRNAs through the ribosome during translation elongation, and that this inhibitory activity is influenced by the presence of modifications at position 37 of the A-site tRNA. Collectively, our study defines the paenilamicins as a new class of context-specific translocation inhibitors.
PubMed: 38826346
DOI: 10.1101/2024.05.21.595107 -
PeerJ 2024American foulbrood (AFB), caused by the highly virulent, spore-forming bacterium , poses a significant threat to honey bee brood. The widespread use of antibiotics not...
BACKGROUND & OBJECTIVES
American foulbrood (AFB), caused by the highly virulent, spore-forming bacterium , poses a significant threat to honey bee brood. The widespread use of antibiotics not only fails to effectively combat the disease but also raises concerns regarding honey safety. The current computational study was attempted to identify a novel therapeutic drug target against , a causative agent of American foulbrood disease in honey bee.
METHODS
We investigated effective novel drug targets through a comprehensive pan-proteome and hierarchal subtractive sequence analysis. In total, 14 strains of genomes were used to identify core genes. Subsequently, the core proteome was systematically narrowed down to a single protein predicted as the potential drug target. Alphafold software was then employed to predict the 3D structure of the potential drug target. Structural docking was carried out between a library of phytochemicals derived from traditional Chinese flora ( > 36,000) and the potential receptor using Autodock tool 1.5.6. Finally, molecular dynamics (MD) simulation study was conducted using GROMACS to assess the stability of the best-docked ligand.
RESULTS
Proteome mining led to the identification of Ketoacyl-ACP synthase III as a highly promising therapeutic target, making it a prime candidate for inhibitor screening. The subsequent virtual screening and MD simulation analyses further affirmed the selection of ZINC95910054 as a potent inhibitor, with the lowest binding energy. This finding presents significant promise in the battle against
CONCLUSIONS
Computer aided drug design provides a novel approach for managing American foulbrood in honey bee populations, potentially mitigating its detrimental effects on both bee colonies and the honey industry.
Topics: Animals; Bees; Paenibacillus larvae; Proteome; Anti-Bacterial Agents; Molecular Docking Simulation; Molecular Dynamics Simulation; Bacterial Proteins
PubMed: 38818453
DOI: 10.7717/peerj.17292 -
Frontiers in Microbiology 2024Legumes are renowned for their distinctive biological characteristic of forming symbiotic associations with soil bacteria, mostly belonging to the familiy, leading to... (Review)
Review
Legumes are renowned for their distinctive biological characteristic of forming symbiotic associations with soil bacteria, mostly belonging to the familiy, leading to the establishment of symbiotic root nodules. Within these nodules, rhizobia play a pivotal role in converting atmospheric nitrogen into a plant-assimilable form. However, it has been discerned that root nodules of legumes are not exclusively inhabited by rhizobia; non-rhizobial endophytic bacteria also reside within them, yet their functions remain incompletely elucidated. This comprehensive review synthesizes available data, revealing that and are the most prevalent genera of nodule endophytic bacteria, succeeded by , , , , and . To date, the bibliographic data available show that followed by and are the main hosts for nodule endophytic bacteria. Clustering analysis consistently supports the prevalence of and as the most abundant nodule endophytic bacteria, alongside , , and . Although non-rhizobial populations within nodules do not induce nodule formation, their presence is associated with various plant growth-promoting properties (PGPs). These properties are known to mediate important mechanisms such as phytostimulation, biofertilization, biocontrol, and stress tolerance, emphasizing the multifaceted roles of nodule endophytes. Importantly, interactions between non-rhizobia and rhizobia within nodules may exert influence on their leguminous host plants. This is particularly shown by co-inoculation of legumes with both types of bacteria, in which synergistic effects on plant growth, yield, and nodulation are often measured. Moreover these effects are pronounced under both stress and non-stress conditions, surpassing the impact of single inoculations with rhizobia alone.
PubMed: 38812696
DOI: 10.3389/fmicb.2024.1386742 -
Microbial Cell Factories May 2024Biosynthesis of metallic nanoparticles using microorganisms are a fabulous and emerging eco-friendly science with well-defined sizes, shapes and controlled... (Comparative Study)
Comparative Study
BACKGROUND
Biosynthesis of metallic nanoparticles using microorganisms are a fabulous and emerging eco-friendly science with well-defined sizes, shapes and controlled monodispersity. Copper nanoparticles, among other metal particles, have sparked increased attention due to their applications in electronics, optics, catalysis, and antimicrobial agents.
RESULTS
This investigation explains the biosynthesis and characterization of copper nanoparticles from soil strains, Niallia circulans G9 and Paenibacillus sp. S4c by an eco-friendly method. The maximum reduction of copper ions and maximum synthesis CuNPs was provided by these strains. Biogenic formation of CuNPs have been characterized by UV-visible absorption spectroscopy, X-ray diffraction, Fourier transform infrared spectroscopy, X-ray analysis and transmission electron microscopy analysis. Using UV-visible spectrum scanning, the synthesised CuNPs' SPR spectra showed maximum absorption peaks at λ. TEM investigation of the produced CuNPs revealed the development of spherical/hexagonal nanoparticles with a size range of 13-100 nm by the G9 strain and spherical nanoparticles with a size range of 5-40 nm by the S4c strain. Functional groups and chemical composition of CuONPs were also confirmed. The antimicrobial activity of the biosynthesized CuNPs were investigated against some human pathogens. CuNPs produced from the G9 strain had the highest activity against Candida albicans ATCC 10,231 and the lowest against Pseudomonas aeruginosa ATCC 9027. CuNPs from the S4c strain demonstrated the highest activity against Escherichia coli ATCC 10,231 and the lowest activity against Klebsiella pneumonia ATCC 13,883.
CONCLUSION
The present work focused on increasing the CuNPs production by two isolates, Niallia circulans G9 and Paenibacillus sp. S4c, which were then characterized alongside. The used analytics and chemical composition techniques validated the existence of CuONPs in the G9 and S4c biosynthesized nano cupper. CuNPs of S4c are smaller and have a more varied shape than those of G9 strain, according to TEM images. In terms of antibacterial activity, the biosynthesized CuNPs from G9 and S4c were found to be more effective against Candida albicans ATCC 10,231 and E. coli ATCC 10,231, respectively.
Topics: Paenibacillus; Metal Nanoparticles; Copper; Anti-Infective Agents; Microbial Sensitivity Tests; Anti-Bacterial Agents; Ascomycota
PubMed: 38802818
DOI: 10.1186/s12934-024-02422-0 -
New Microbes and New Infections Jun 2024
PubMed: 38799939
DOI: 10.1016/j.nmni.2024.101372 -
New Microbes and New Infections Jun 2024
Expression of Concern: Noncontiguous finished genome sequences and descriptions of Paenibacillus bouchesdurhonensis,' Paenibacillus rubinfantis,' Paenibacillus senegalimassiliensis' and Paenibacillus tuaregi' identified by culturomics.
PubMed: 38799856
DOI: 10.1016/j.nmni.2024.101366 -
New Microbes and New Infections Jun 2024
PubMed: 38799841
DOI: 10.1016/j.nmni.2024.101362 -
Biochar 2024While many studies have examined the role of biochar in carbon (C) accrual in short-term scale, few have explored the decadal scale influences of biochar on non-biochar...
Distinct biophysical and chemical mechanisms governing sucrose mineralization and soil organic carbon priming in biochar amended soils: evidence from 10 years of field studies.
UNLABELLED
While many studies have examined the role of biochar in carbon (C) accrual in short-term scale, few have explored the decadal scale influences of biochar on non-biochar C, e.g., native soil organic C (SOC) and added substrate. To address this knowledge gap, soils were collected from decade-old biochar field trials located in the United Kingdom (Cambisol) and China (Fluvisol), with each site having had three application rates (25-30, 50-60 and 75-100 Mg ha) of biochar plus an unamended Control, applied once in 2009. We assessed physicochemical and microbial properties associated with sucrose (representing the rhizodeposits) mineralization and the priming effect (PE) on native SOC. Here, we showed both soils amended with biochar at the middle application rate (50 Mg ha biochar in Cambisol and 60 Mg ha biochar in Fluvisol) resulted in greater substrate mineralization. The enhanced accessibility and availability of sucrose to microorganisms, particularly fast-growing bacterial genera like and (r-strategists belonging to the Proteobacteria and Firmicutes phyla, respectively), can be attributed to the improved physicochemical properties of the soil, including pH, porosity, and pore connectivity, as revealed by synchrotron-based micro-CT. Random forest analysis also confirmed the contribution of the microbial diversity and physical properties such as porosity on sucrose mineralization. Biochar at the middle application rate, however, resulted in the lowest PE (0.3 and 0.4 mg of CO-C g soil in Cambisol and Fluvisol, respectively) after 53 days of incubation. This result might be associated with the fact that the biochar promoted large aggregates formation, which enclosed native SOC in soil macro-aggregates (2-0.25 mm). Our study revealed a diverging pattern between substrate mineralization and SOC priming linked to the biochar application rate. This suggests distinct mechanisms, biophysical and physicochemical, driving the mineralization of non-biochar carbon in a field where biochar was applied a decade before.
SUPPLEMENTARY INFORMATION
The online version contains supplementary material available at 10.1007/s42773-024-00327-0.
PubMed: 38799721
DOI: 10.1007/s42773-024-00327-0