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Microorganisms May 2024Polycyclic aromatic hydrocarbons (PAHs) cause serious stress to biological health and the soil environment as persistent pollutants. Despite the wide use of biochar in...
Polycyclic aromatic hydrocarbons (PAHs) cause serious stress to biological health and the soil environment as persistent pollutants. Despite the wide use of biochar in promoting soil improvement, the mechanism of biochar removing soil PAHs through rhizosphere effect in the process of phytoremediation remain uncertain. In this study, the regulation of soil niche and microbial degradation strategies under plants and biochar were explored by analyzing the effects of plants and biochar on microbial community composition, soil metabolism and enzyme activity in the process of PAH degradation. The combination of plants and biochar significantly increased the removal of phenanthrene (6.10%), pyrene (11.50%), benzo[a]pyrene (106.02%) and PAHs (27.10%) when compared with natural attenuation, and significantly increased the removal of benzo[a]pyrene (34.51%) and PAHs (5.96%) when compared with phytoremediation. Compared with phytoremediation, the combination of plants and biochar significantly increased soil nutrient availability, enhanced soil enzyme activity (urease and catalase), improved soil microbial carbon metabolism and amino acid metabolism, thereby benefiting microbial resistance to PAH stress. In addition, the activity of soil enzymes (dehydrogenase, polyphenol oxidase and laccase) and the expression of genes involved in the degradation and microorganisms (, , and ) were up-regulated through the combined action of plants and biochar. In view of the aforementioned results, the combined application of plants and biochar can enhance the degradation of PAHs and alleviate the stress of PAH on soil microorganisms.
PubMed: 38792797
DOI: 10.3390/microorganisms12050968 -
Molecules (Basel, Switzerland) May 2024Environmental pollution stands as one of the significant global challenges we face today. Polycyclic aromatic hydrocarbons (PAHs), a class of stubborn organic...
Environmental pollution stands as one of the significant global challenges we face today. Polycyclic aromatic hydrocarbons (PAHs), a class of stubborn organic pollutants, have long been a focal point of bioremediation research. This study aims to explore the impact and mechanisms of graphene oxide (GO) on the phytoremediation effectiveness of PAHs. The results underscore the significant efficacy of GO in accelerating the degradation of PAHs. Additionally, the introduction of GO altered the diversity and community structure of endophytic bacteria within the roots, particularly those genera with potential for PAH degradation. Through LEfSe analysis and correlation studies, we identified specific symbiotic bacteria, such as , , , , , , and , which coexist and interact under the influence of GO, synergistically degrading PAHs. These bacteria may serve as key biological markers in the PAH degradation process. These findings provide new theoretical and practical foundations for the application of nanomaterials in plant-based remediation of polluted soils and showcase the immense potential of plant-microbe interactions in environmental restoration.
Topics: Graphite; Polycyclic Aromatic Hydrocarbons; Soil Pollutants; Biodegradation, Environmental; Soil Microbiology; Bacteria; Endophytes; Plant Roots; Sphingomonas; Plants; Mycobacterium; Flavobacterium; Streptomyces; Microbacterium
PubMed: 38792204
DOI: 10.3390/molecules29102342 -
Foods (Basel, Switzerland) May 2024Microbial nitrogen sources are promising, and soy protein as a plant-based nitrogen source has absolute advantages in creating microbial culture medium in terms of...
Microbial nitrogen sources are promising, and soy protein as a plant-based nitrogen source has absolute advantages in creating microbial culture medium in terms of renewability, eco-friendliness, and greater safety. Soy protein is rich in variety due to different extraction technologies and significantly different in the cell growth and metabolism of microorganisms as nitrogen source. Therefore, different soy proteins (soy meal powder, SMP; soy peptone, SP; soy protein concentrate, SPC; soy protein isolate, SPI; and soy protein hydrolysate, SPH) were used as nitrogen sources to culture , , and to evaluate the suitable soy nitrogen sources of the above strains. The results showed that had the highest bacteria density in SMP medium; had the highest bacteria density in SPI medium; and had the highest PMV in SPI medium. Nattokinase activity was the highest in SP medium; the bacteriostatic effect of nisin was the best in SPI medium; and the clavulanic acid concentration was the highest in SMP medium. Based on analyzing the correlation between the nutritional composition and growth metabolism of the strains, the results indicated that the protein content and amino acid composition were the key factors influencing the cell growth and metabolism of the strains. These findings present a new, high-value application opportunity for soybean protein.
PubMed: 38790825
DOI: 10.3390/foods13101525 -
Microbial Cell Factories May 2024Streptomyces is renowned for its robust biosynthetic capacity in producing medically relevant natural products. However, the majority of natural products biosynthetic...
BACKGROUND
Streptomyces is renowned for its robust biosynthetic capacity in producing medically relevant natural products. However, the majority of natural products biosynthetic gene clusters (BGCs) either yield low amounts of natural products or remain cryptic under standard laboratory conditions. Various heterologous production hosts have been engineered to address these challenges, and yet the successful activation of BGCs has still been limited. In our search for a valuable addition to the heterologous host panel, we identified the strain Streptomyces sp. A4420, which exhibited rapid initial growth and a high metabolic capacity, prompting further exploration of its potential.
RESULTS
We engineered a polyketide-focused chassis strain based on Streptomyces sp. A4420 (CH strain) by deleting 9 native polyketide BGCs. The resulting metabolically simplified organism exhibited consistent sporulation and growth, surpassing the performance of most existing Streptomyces based chassis strains in standard liquid growth media. Four distinct polyketide BGCs were chosen and expressed in various heterologous hosts, including the Streptomyces sp. A4420 wild-type and CH strains, alongside Streptomyces coelicolor M1152, Streptomyces lividans TK24, Streptomyces albus J1074, and Streptomyces venezuelae NRRL B-65442. Remarkably, only the Streptomyces sp. A4420 CH strain demonstrated the capability to produce all metabolites under every condition outperforming its parental strain and other tested organisms. To enhance visualization and comparison of the tested strains, we developed a matrix-like analysis involving 15 parameters. This comprehensive analysis unequivocally illustrated the significant potential of the new strain to become a popular heterologous host.
CONCLUSION
Our engineered Streptomyces sp. A4420 CH strain exhibits promising attributes for the heterologous expression of natural products with a focus on polyketides, offering an alternative choice in the arsenal of heterologous production strains. As genomics and cloning strategies progress, establishment of a diverse panel of heterologous production hosts will be crucial for expediting the discovery and production of medically relevant natural products derived from Streptomyces.
Topics: Streptomyces; Multigene Family; Biological Products; Polyketides; Metabolic Engineering; Streptomyces coelicolor; Streptomyces lividans; Biosynthetic Pathways
PubMed: 38790014
DOI: 10.1186/s12934-024-02416-y -
Nature Communications May 2024Contractile injection systems (CISs) are prokaryotic phage tail-like nanostructures loading effector proteins that mediate various biological processes. Although CIS...
Contractile injection systems (CISs) are prokaryotic phage tail-like nanostructures loading effector proteins that mediate various biological processes. Although CIS functions have been diversified through evolution and hold the great potential as protein delivery systems, the functional characterisation of CISs and their effectors is currently limited to a few CIS lineages. Here, we show that the CISs of Streptomyces davawensis belong to a unique group of bacterial CISs distributed across distant phyla and facilitate sporogenic differentiation of this bacterium. CIS loss results in decreases in extracellular DNA release, biomass accumulation, and spore formation in S. davawensis. CISs load an effector, which is a remote homolog of phage tapemeasure proteins, and its C-terminal domain has endonuclease activity responsible for the CIS-associated phenotypes. Our findings illustrate that CISs can contribute to the reproduction of bacteria through the action of the effector and suggest an evolutionary link between CIS effectors and viral cargos.
Topics: Streptomyces; Bacteriophages; Spores, Bacterial; Bacterial Proteins; Phylogeny; Viral Proteins; Viral Tail Proteins
PubMed: 38789435
DOI: 10.1038/s41467-024-48834-9 -
Waste Management (New York, N.Y.) Jun 2024This study aims to investigate the microbiological working environment of biowaste workers, focusing on airborne fungal and bacterial species exposure, size...
This study aims to investigate the microbiological working environment of biowaste workers, focusing on airborne fungal and bacterial species exposure, size distribution, and species on workers' hands. The research, conducted across six plants with 45 personal exposure assessments, revealed a total of 150 bacterial species and 47 fungal species on workers' hands, including 19 and 9 species classified in risk class 2 (RC2), respectively. Workers' exposure analysis identified 172 bacterial and 32 fungal species, with several in RC2. In work areas, 55 anaerobic bacterial species belonging to RC2 were found. Different species compositions were observed in various particle size fractions, with the highest species richness for anaerobic bacteria in the fraction potentially depositing in the secondary bronchi and for fungi in the pharynx fraction. The geometric mean aerodynamic diameter (D) of RC2 anaerobic bacteria was 3.9 µm, <1.6 µm for Streptomyces, 3.4 µm for Aspergillus, and 2.0 µm for Penicillium. Overlapping species were identified on workers' hands, in their exposure, and in work areas, with Bacillus amyloliquefaciens, Leuconostoc mesenteroides, Bacillus cereus, Enterococcus casseliflavus, and Aspergillus niger consistently present. While the majority of RC2 bacterial species lacked documented associations with occupational health problems, certain bacteria and fungi, including Bacillus cereus, Escherichia coli, Enterobacter, Klebsiella pneumonia, Aspergillus fumigatus, Aspergillus niger, Aspergillus flavus, Lichtheimia corymbifera, Lichtheimia ramosa, and Paecilomyces variotii, have previously been linked to occupational health issues. In conclusion, biowaste workers were exposed to a wide range of microorganisms including RC2 species which would deposit in different parts of the airways.
Topics: Humans; Fungi; Bacteria; Occupational Exposure; Air Microbiology; Hand; Environmental Monitoring; Inhalation Exposure; Air Pollutants, Occupational
PubMed: 38788497
DOI: 10.1016/j.wasman.2024.05.018 -
Journal of Fungi (Basel, Switzerland) Apr 2024Gray mold, caused by , poses significant threats to various crops, while it can be remarkably inhibited by ε-poly-L-lysine (ε-PL). A previous study found that...
Gray mold, caused by , poses significant threats to various crops, while it can be remarkably inhibited by ε-poly-L-lysine (ε-PL). A previous study found that extracts could stimulate the ε-PL biosynthesis of , while it is unclear whether the impact of the signal on ε-PL biosynthesis is direct or indirect. This study evaluated the role of elevated reactive oxygen species (ROS) in efficient ε-PL biosynthesis after induction, and its underlying mechanism was disclosed with a transcriptome analysis. The microbial call from could arouse ROS elevation in cells, which fall in a proper level that positively influenced the ε-PL biosynthesis. A systematic transcriptional analysis revealed that this proper dose of intracellular ROS could induce a global transcriptional promotion on key pathways in ε-PL biosynthesis, including the embden-meyerhof-parnas pathway, the pentose phosphate pathway, the tricarboxylic acid cycle, the diaminopimelic acid pathway, ε-PL accumulation, cell respiration, and energy synthesis, in which sigma factor HrdD and the transcriptional regulators of TcrA, TetR, FurA, and MerR might be involved. In addition, the intracellular ROS elevation also resulted in a global modification of secondary metabolite biosynthesis, highlighting the secondary signaling role of intracellular ROS in ε-PL production. This work disclosed the transcriptional mechanism of efficient ε-PL production that resulted from an intracellular ROS elevation after elicitors' induction, which was of great significance in industrial ε-PL production as well as the biocontrol of gray mold disease.
PubMed: 38786679
DOI: 10.3390/jof10050324 -
Marine Drugs May 2024Naturally occurring echinocandin B and FR901379 are potent antifungal lipopeptides featuring a cyclic hexapeptide nucleus and a fatty acid side chain. They are the...
Naturally occurring echinocandin B and FR901379 are potent antifungal lipopeptides featuring a cyclic hexapeptide nucleus and a fatty acid side chain. They are the parent compounds of echinocandin drugs for the treatment of severe fungal infections caused by the and species. To minimize hemolytic toxicity, the native fatty acid side chains in these drug molecules are replaced with designer acyl side chains. The deacylation of the -acyl side chain is, therefore, a crucial step for the development and manufacturing of echinocandin-type antibiotics. Echinocandin E (ECE) is a novel echinocandin congener with enhanced stability generated via the engineering of the biosynthetic machinery of echinocandin B (ECB). In the present study, we report the discovery of the first echinocandin E acylase (ECEA) using the enzyme similarity tool (EST) for enzymatic function mining across protein families. ECEA is derived from sp. SY1965 isolated from a sediment collected from the Mariana Trench. It was cloned and heterologously expressed in TK24. The resultant TKecea66 strain showed efficient cleavage activity of the acyl side chain of ECE, showing promising applications in the development of novel echinocandin-type therapeutics. Our results also provide a showcase for harnessing the essentially untapped biodiversity from the hadal ecosystems for the discovery of functional molecules.
Topics: Streptomyces; Echinocandins; Antifungal Agents; Amidohydrolases; Fungal Proteins
PubMed: 38786603
DOI: 10.3390/md22050212 -
Marine Drugs Apr 2024Marine symbiotic and epiphyte microorganisms are sources of bioactive or structurally novel natural products. Metabolic blockade-based genome mining has been proven to...
Metabolic Blockade-Based Genome Mining of Sea Anemone-Associated sp. S1502 Identifies Atypical Angucyclines WS-5995 A-E: Isolation, Identification, Biosynthetic Investigation, and Bioactivities.
Marine symbiotic and epiphyte microorganisms are sources of bioactive or structurally novel natural products. Metabolic blockade-based genome mining has been proven to be an effective strategy to accelerate the discovery of natural products from both terrestrial and marine microorganisms. Here, the metabolic blockade-based genome mining strategy was applied to the discovery of other metabolites in a sea anemone-associated sp. S1502. We constructed a mutant sp. S1502/Δ that switched to producing the atypical angucyclines WS-5995 A-E, among which WS-5995 E is a new compound. A biosynthetic gene cluster () of the angucyclines was identified through gene knock-out and heterologous expression studies. The biosynthetic pathways of WS-5995 A-E were proposed, the roles of some tailoring and regulatory genes were investigated, and the biological activities of WS-5995 A-E were evaluated. WS-5995 A has significant anti- activity with an IC value of 2.21 μM. The production of antibacterial streptopyrroles and anticoccidial WS-5995 A-E may play a protective role in the mutual relationship between sp. S1502 and its host.
Topics: Streptomyces; Animals; Sea Anemones; Multigene Family; Anti-Bacterial Agents; Biosynthetic Pathways; Genome, Bacterial; Biological Products; Anthraquinones; Angucyclines and Angucyclinones
PubMed: 38786587
DOI: 10.3390/md22050195 -
Antibiotics (Basel, Switzerland) May 2024Actinomycetes have long been recognized as important sources of clinical antibiotics. However, the exploration of rare actinomycetes, despite their potential for...
Actinomycetes have long been recognized as important sources of clinical antibiotics. However, the exploration of rare actinomycetes, despite their potential for producing bioactive molecules, has remained relatively limited compared to the extensively studied genus. The extensive investigation of species and their natural products has led to a diminished probability of discovering novel bioactive compounds from this group. Consequently, our research focus has shifted towards less explored actinomycetes, beyond , with particular emphasis on (). The genome of was annotated and analyzed through whole-genome sequencing using multiple bio-informatics tools, revealing an 8.6 Mbp genome with a 74.42% G + C content. AntiSMASH analysis identified 40 putative biosynthetic gene clusters (BGCs), approximately half of which were recessive and unknown. Additionally, metabolomic mining utilizing mass spectrometry demonstrated the potential for this rare actinomycete to generate numerous bioactive compounds such as glycosides and macrolides, with bafilomycin being the major compound produced. Collectively, genomics- and metabolomics-based techniques confirmed 's potential as a bioactive secondary metabolite producer that is worthy of further exploration.
PubMed: 38786187
DOI: 10.3390/antibiotics13050459