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Frontiers in Microbiology 2024With more than 100 rubber-degrading strains being reported, only 9 Lcp proteins isolated from , and have been purified and biochemically characterized. A new strain,...
With more than 100 rubber-degrading strains being reported, only 9 Lcp proteins isolated from , and have been purified and biochemically characterized. A new strain, Dactylosporangium sp. AC04546 (strain JCM34239), isolated from soil samples collected in Sarawak Forest, was able to grow and utilize natural or synthetic rubber as the sole carbon source. Complete genome of Strain AC04546 was obtained from the hybrid assembly of PacBio Sequel II and Illumina MiSeq. Strain AC04546 has a large circular genome of 13.08 Mb with a G+C content of 72.1%. The genome contains 11,865 protein-coding sequences with 3 latex clearing protein () genes located on its chromosome. The genetic organization of the gene cluster is similar to two other reported rubber-degrading strains- sp. OR16 and Streptomyces sp. CFMR 7. All 3 Lcp from strain AC04546 were expressed in and exhibited degrading activity against natural rubber. The distinctiveness of strain AC04546, along with other characterized rubber-degrading strains, is reported here.
PubMed: 38873160
DOI: 10.3389/fmicb.2024.1378082 -
BMC Plant Biology Jun 2024Apple Replant Disease (ARD) is common in major apple-growing regions worldwide, but the role of rhizosphere microbiota in conferring ARD resistance and promoting plant...
BACKGROUND
Apple Replant Disease (ARD) is common in major apple-growing regions worldwide, but the role of rhizosphere microbiota in conferring ARD resistance and promoting plant growth remains unclear.
RESULTS
In this study, a synthetic microbial community (SynCom) was developed to enhance apple plant growth and combat apple pathogens. Eight unique bacteria selected via microbial culture were used to construct the antagonistic synthetic community, which was then inoculated into apple seedlings in greenhouse experiments. Changes in the rhizomicroflora and the growth of aboveground plants were monitored. The eight strains, belonging to the genera Bacillus and Streptomyces, have the ability to antagonize pathogens such as Fusarium oxysporum, Rhizoctonia solani, Botryosphaeria ribis, and Physalospora piricola. Additionally, these eight strains can stably colonize in apple rhizosphere and some of them can produce siderophores, ACC deaminase, and IAA. Greenhouse experiments with Malus hupehensis Rehd indicated that SynCom promotes plant growth (5.23%) and increases the nutrient content of the soil, including soil organic matter (9.25%) and available K (1.99%), P (7.89%), and N (0.19%), and increases bacterial richness and the relative abundance of potentially beneficial bacteria. SynCom also increased the stability of the rhizosphere microbial community, the assembly of which was dominated by deterministic processes (|β NTI| > 2).
CONCLUSIONS
Our results provide insights into the contribution of the microbiome to pathogen inhibition and host growth. The formulation and manipulation of similar SynComs may be a beneficial strategy for promoting plant growth and controlling soil-borne disease.
Topics: Malus; Plant Diseases; Rhizosphere; Soil Microbiology; Microbiota; Rhizoctonia; Biological Control Agents; Bacillus; Antibiosis
PubMed: 38872113
DOI: 10.1186/s12870-024-05253-8 -
Antimicrobial Agents and Chemotherapy Jun 2024Neglected tropical diseases caused by trypanosomatid parasites have devastating health and economic consequences, especially in tropical areas. New drugs or new...
Neglected tropical diseases caused by trypanosomatid parasites have devastating health and economic consequences, especially in tropical areas. New drugs or new combination therapies to fight these parasites are urgently needed. Venturicidin A, a macrolide extracted from , inhibits the ATP synthase complex of fungi and bacteria. However, its effect on trypanosomatids is not fully understood. In this study, we tested venturicidin A on a panel of trypanosomatid parasites using Alamar Blue assays and found it to be highly active against and , but much less so against . Using fluorescence microscopy, we observed a rapid loss of the mitochondrial membrane potential in bloodstream forms upon venturicidin A treatment. Additionally, we report the loss of mitochondrial DNA in approximately 40%-50% of the treated parasites. We conclude that venturicidin A targets the ATP synthase of , and we suggest that this macrolide could be a candidate for anti-trypanosomatid drug repurposing, drug combinations, or medicinal chemistry programs.
PubMed: 38869301
DOI: 10.1128/aac.01671-23 -
Polyester degradation by soil bacteria: identification of conserved BHETase enzymes in Streptomyces.Communications Biology Jun 2024The rising use of plastic results in an appalling amount of waste which is scattered into the environment. One of these plastics is PET which is mainly used for bottles....
The rising use of plastic results in an appalling amount of waste which is scattered into the environment. One of these plastics is PET which is mainly used for bottles. We have identified and characterized an esterase from Streptomyces, annotated as LipA, which can efficiently degrade the PET-derived oligomer BHET. The Streptomyces coelicolor ScLipA enzyme exhibits varying sequence similarity to several BHETase/PETase enzymes, including IsPETase, TfCut2, LCC, PET40 and PET46. Of 96 Streptomyces strains, 18% were able to degrade BHET via one of three variants of LipA, named ScLipA, S2LipA and S92LipA. SclipA was deleted from S. coelicolor resulting in reduced BHET degradation. Overexpression of all LipA variants significantly enhanced BHET degradation. All variants were expressed in E. coli for purification and biochemical analysis. The optimum conditions were determined as pH 7 and 25 °C for all variants. The activity on BHET and amorphous PET film was investigated. S2LipA efficiently degraded BHET and caused roughening and indents on the surface of PET films, comparable to the activity of previously described TfCut2 under the same conditions. The abundance of the S2LipA variant in Streptomyces suggests an environmental advantage towards the degradation of more polar substrates including these polluting plastics.
Topics: Streptomyces; Soil Microbiology; Bacterial Proteins; Biodegradation, Environmental; Streptomyces coelicolor; Esterases; Polyethylene Terephthalates
PubMed: 38867087
DOI: 10.1038/s42003-024-06414-z -
Nature Communications Jun 2024Ferroptosis is an iron-dependent cell death that was discovered recently. For beneficial microbes to establish mutualistic relationships with hosts, precisely controlled...
Ferroptosis is an iron-dependent cell death that was discovered recently. For beneficial microbes to establish mutualistic relationships with hosts, precisely controlled cell death in plant cells is necessary. However, whether ferroptosis is involved in the endophyte‒plant system is poorly understood. Here, we reported that endophytic Streptomyces hygroscopicus OsiSh-2, which established a sophisticated and beneficial interaction with host rice plants, caused ferroptotic cell death in rice characterized by ferroptosis- and immune-related markers. Treatments with ferroptosis inhibitors and inducers, different doses of OsiSh-2, and the siderophore synthesis-deficient mutant ΔcchH revealed that only moderate ferroptosis induced by endophytes is essential for the establishment of an optimal symbiont to enhance plant growth. Additionally, ferroptosis involved in a defence-primed state in rice, which contributed to improved resistance against rice blast disease. Overall, our study provides new insights into the mechanisms of endophyte‒plant interactions mediated by ferroptosis and suggests new directions for crop yield promotion.
Topics: Oryza; Ferroptosis; Endophytes; Disease Resistance; Plant Diseases; Symbiosis; Streptomyces; Siderophores; Iron
PubMed: 38866764
DOI: 10.1038/s41467-024-49099-y -
Protein Science : a Publication of the... Jul 2024A common evolutionary mechanism in biology to drive function is protein oligomerization. In prokaryotes, the symmetrical assembly of repeating protein units to form...
A common evolutionary mechanism in biology to drive function is protein oligomerization. In prokaryotes, the symmetrical assembly of repeating protein units to form homomers is widespread, yet consideration in vitro of whether such assemblies have functional or mechanistic consequences is often overlooked. Dye-decolorizing peroxidases (DyPs) are one such example, where their dimeric α + β barrel units can form various oligomeric states, but the oligomer influence, if any, on mechanism and function has received little attention. In this work, we have explored the oligomeric state of three DyPs found in Streptomyces lividans, each with very different mechanistic behaviors in their reactions with hydrogen peroxide and organic substrates. Using analytical ultracentrifugation, we reveal that except for one of the A-type DyPs where only a single sedimenting species is detected, oligomer states ranging from homodimers to dodecamers are prevalent in solution. Using cryo-EM on preparations of the B-type DyP, we determined a 3.02 Å resolution structure of a hexamer assembly that corresponds to the dominant oligomeric state in solution as determined by analytical ultracentrifugation. Furthermore, cryo-EM data detected sub-populations of higher-order oligomers, with one of these formed by an arrangement of two B-type DyP hexamers to give a dodecamer assembly. Our solution and structural insights of these oligomer states provide a new framework to consider previous mechanistic studies of these DyP members and are discussed in terms of long-range electron transfer for substrate oxidation and in the "storage" of oxidizable equivalents on the heme until a two-electron donor is available.
Topics: Streptomyces lividans; Oxidation-Reduction; Peroxidases; Protein Multimerization; Coloring Agents; Bacterial Proteins; Models, Molecular; Substrate Specificity; Cryoelectron Microscopy; Hydrogen Peroxide
PubMed: 38864770
DOI: 10.1002/pro.5073 -
Microbiology Spectrum Jun 2024Clorobiocin is a well-known, highly effective inhibitor of DNA gyrase belonging to the aminocoumarin antibiotics. To identify potentially novel derivatives of this...
UNLABELLED
Clorobiocin is a well-known, highly effective inhibitor of DNA gyrase belonging to the aminocoumarin antibiotics. To identify potentially novel derivatives of this natural product, we conducted an untargeted investigation of clorobiocin biosynthesis in the known producer DS 12.976 using LC-MS, molecular networking, and analysis of fragmentation spectra. Previously undescribed clorobiocin derivatives uncovered in this study include bromobiocin, a variant halogenated with bromine instead of chlorine, hydroxylated clorobiocin, carrying an additional hydroxyl group on its 5-methyl-pyrrole 2-carboxyl moiety, and two other derivatives with modifications on their 3-dimethylallyl 4-hydroxybenzoate moieties. Furthermore, we identified several compounds not previously considered clorobiocin pathway products, which provide new insights into the clorobiocin biosynthetic pathway. By supplementing the medium with different concentrations of potassium bromide, we confirmed that the clorobiocin halogenase can utilize bromine instead of chlorine. The reaction, however, is impeded such that non-halogenated clorobiocin derivatives accumulate. Preliminary assays indicate that the antibacterial activity of bromobioin against and efflux-impaired matches that of clorobiocin. Our findings emphasize that yet unexplored compounds can be discovered from established strains and biosynthetic gene clusters by means of metabolomics analysis and highlight the utility of LC-MS-based methods to contribute to unraveling natural product biosynthetic pathways.
IMPORTANCE
The aminocoumarin clorobiocin is a well-known gyrase inhibitor produced by the gram-positive bacterium DS 12.976. To gain a deeper understanding of the biosynthetic pathway of this complex composite of three chemically distinct entities and the product spectrum, we chose a metabolite-centric approach. Employing high-resolution LC-MS analysis, we investigated the pathway products in extracted culture supernatants of the natural producer. Novel pathway products were identified that expand our understanding of three aspects of the biosynthetic pathway, namely the modification of the noviose, transfer and methylation of the pyrrole 2-carboxyl moiety, and halogenation. For the first time, brominated products were detected. Their levels and the levels of non-halogenated products increased in medium supplemented with KBr. Based on the presented data, we propose that the enzyme promiscuity contributes to a broad product spectrum.
PubMed: 38864648
DOI: 10.1128/spectrum.00423-24 -
MSphere Jun 2024is a necrotrophic phytopathogen able to attack more than 200 different plant species causing strong yield losses worldwide. Many synthetic fungicides have been...
UNLABELLED
is a necrotrophic phytopathogen able to attack more than 200 different plant species causing strong yield losses worldwide. Many synthetic fungicides have been developed to control this disease, resulting in the rise of fungicide-resistance strains. The aim of this study was to identify strains showing antagonistic activity against to contribute to plant protection in an environmentally friendly way. We isolated 15 Actinomycete strains from 9 different Swiss soils. The culture filtrates of three isolates showing antifungal activity inhibited spore germination and delayed mycelial growth of . Infection experiments showed that plants were more resistant to this pathogen after leaf treatment with the filtrates. Bioassay-guided isolation of the active compounds revealed the presence of germicidins A and B as well as of oligomycins A, B, and E. While germicidins were mostly inactive, oligomycin B reduced the mycelial growth of significantly. Moreover, all three oligomycins inhibited this fungus' spore germination, suggesting that these molecules might contribute to the 's ability to protect plants against infection by the broad host-pathogen .
IMPORTANCE
This study reports the isolation of new strains with strong plant-protective potential mediated by their production of specialized metabolites. Using the broad host range pathogenic fungus , we demonstrate that the cell-free filtrate of selected isolates efficiently inhibits different developmental stages of the fungus, including mycelial growth and the epidemiologically relevant spore germination. Beyond experiments, the strains and their metabolites also efficiently protected plants against the disease caused by this pathogen. This work further identifies oligomycins as active compounds involved in the observed antifungal activity of the strains. This work shows that we can harness the natural ability of soil-borne microbes and of their metabolites to efficiently fight other microbes responsible for significant crop losses. This opens the way to the development of environmentally friendly health protection measures for crops of agronomical relevance, based on these newly isolated strains or their metabolic extracts containing oligomycins.
PubMed: 38864637
DOI: 10.1128/msphere.00667-23 -
BMC Microbiology Jun 2024Antimicrobial resistance (AMR) is a serious worldwide public health concern that needs immediate action. Probiotics could be a promising alternative for fighting...
BACKGROUND
Antimicrobial resistance (AMR) is a serious worldwide public health concern that needs immediate action. Probiotics could be a promising alternative for fighting antibiotic resistance, displaying beneficial effects to the host by combating diseases, improving growth, and stimulating the host immune responses against infection. This study was conducted to evaluate the probiotic, antibacterial, and antibiofilm potential of Streptomyces levis strain HFM-2 isolated from the healthy human gut.
RESULTS
In vitro antibacterial activity in the cell-free supernatant of S. levis strain HFM-2 was evaluated against different pathogens viz. K. pneumoniae sub sp. pneumoniae, S. aureus, B. subtilis, VRE, S. typhi, S. epidermidis, MRSA, V. cholerae, M. smegmatis, E. coli, P. aeruginosa and E. aerogenes. Further, the ethyl acetate extract from S. levis strain HFM-2 showed strong biofilm inhibition against S. typhi, K. pneumoniae sub sp. pneumoniae, P. aeruginosa and E. coli. Fluorescence microscopy was used to detect biofilm inhibition properties. MIC and MBC values of EtOAc extract were determined at 500 and 1000 µg/mL, respectively. Further, strain HFM-2 showed high tolerance in gastric juice, pancreatin, bile, and at low pH. It exhibited efficient adhesion properties, displaying auto-aggregation (97.0%), hydrophobicity (95.71%, 88.96%, and 81.15% for ethyl acetate, chloroform and xylene, respectively), and showed 89.75%, 86.53%, 83.06% and 76.13% co-aggregation with S. typhi, MRSA, S. pyogenes and E. coli, respectively after 60 min of incubation. The S. levis strain HFM-2 was susceptible to different antibiotics such as tetracycline, streptomycin, kanamycin, ciprofloxacin, erythromycin, linezolid, meropenem, amikacin, gentamycin, clindamycin, moxifloxacin and vancomycin, but resistant to ampicillin and penicillin G.
CONCLUSION
The study shows that S. levis strain HFM-2 has significant probiotic properties such as good viability in bile, gastric juice, pancreatin environment, and at low pH; proficient adhesion properties, and antibiotic susceptibility. Further, the EtOAc extract of Streptomyces levis strain HFM-2 has a potent antibiofilm and antibacterial activity against antibacterial-resistant clinical pathogens.
Topics: Biofilms; Humans; Probiotics; Streptomyces; Microbial Sensitivity Tests; Anti-Bacterial Agents; Bacteria; Gastrointestinal Tract
PubMed: 38862894
DOI: 10.1186/s12866-024-03353-x -
Plant Disease Jun 2024Severe typical deep-pitted lesions of Potato Common Scab (PCS) disease were observed in two locations in China, Dingxi, Gansu Province, and Shuozhou, Shaanxi Province,...
Severe typical deep-pitted lesions of Potato Common Scab (PCS) disease were observed in two locations in China, Dingxi, Gansu Province, and Shuozhou, Shaanxi Province, in 2021. Potato farms in Dingxi growing cultivar Huangxin 226 (26 hectares) exhibited a scab disease incidence of 10%, while cultivar Jinshu 15# (4 hectares) in Shuozhou showed a disease incidence of 30% (Fig. 1). During harvest, tubers displaying PCS symptoms were collected for pathogen isolation. To obtain pathogen isolates, surface-sterilized tuber tissue with scab lesions was ground in sterile water, serially diluted, and plated onto ISP5 agar medium plates (Handique et al. 2022). Five pure colonies of Streptomyces isolate were obtained, designated as ZRIMU1503, ZRIMU1502, ZRIMU1320, ZRIMU1321and ZRIMU791. Genomic DNA was extracted and sequenced using Illumina technology. Sequencing data of the 5 isolates were uploaded to NCBI GenBank and annotated (Accession numbers: JBBAYL010000000, JBBAYM010000000, JBBAYN010000000, JBBAYO010000000 and JBBAYP010000000, respectively) using the PGAP pipeline (Tatusova et al. 2016). Average Nucleotide Identity (ANI) values (97.52 %, 97.53 %,97.54 %,97.57 % and 97.52 %, respectively) indicated the identity of the five isolates to the type strain S. brasiliscabiei IBSBF 2867T. Additionally, pairwise comparisons of Digital DNA Hybridization (DDH) value (76.2%, 76.3%, 76.4%, 76.4% and 76.2% respectively) of all the Streptomyces type strains show the highest identity to S. brasiliscabiei IBSBF 2867T. Twelve housekeeping genes (acnA, atpD, dnaN, gap, gyrA, gyrB , infB, mdh, recA, rplB, rpoB, and trpB) were extracted from the genome sequence of the five isolates to construct a multi-locus sequence analysis (MLSA) tree. The evolutionary distance of the five isolates was constructed using MEGAX software (Kumar et al., 1994), along with other Streptomyces strains that are known to cause PCS. The resulting cladogram demonstrated the isolated strains clustered together with S. brasiliscabiei IBSBF 2867T (Fig.2). Koch's postulates were fulfilled by inoculating a perlite potting mix with spore suspensions of each isolate (104 CFU/ml), planting tubers (cv. Favorita), and reproducing PCS symptoms at harvest after three months. Negative control received water treatment. The plants were kept in greenhouse with 12 h of light per day and irrigated regularly. The experiment was repeated twice, once in April 2022 and again in April 2023. On harvest, all five isolates exhibited development of severe symptoms of PCS (Fig.1), while the negative controls had no lesions. The pathogen was reisolated from the lesions and confirmed to be identical to the original isolate by 16S rRNA gene sequences. To our knowledge, this is the first report of S. brasiliscabiei causing PCS in China. S. brasiliscabiei was identified as a new species to cause PCS in Brazil and was identified based on morphology, pathogenicity, and genetic features (Corrêa et al. 2021). Multiple pathogen-causing PCS has been recognized in China and a surge of disease incidence in potato fields has been reported (Handique et al. 2022; Wu et al. 2023). S. brasiliscabiei causes severe symptoms which makes potatoes unmarketable. The disease epidemiology of this pathogen needs to be investigated.
PubMed: 38861470
DOI: 10.1094/PDIS-03-24-0607-PDN