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Journal of Applied Microbiology Sep 2021This research investigated the influence of soil microbiota on Escherichia coli O157:H7 survival in soil rinse and artificial soil. Additionally, the influence of...
AIMS
This research investigated the influence of soil microbiota on Escherichia coli O157:H7 survival in soil rinse and artificial soil. Additionally, the influence of selected soil bacteria on E. coli O157:H7 in soil environments was determined.
METHODS AND RESULTS
Escherichia coli O157:H7 counts (log CFU per ml or g ) were determined by spread plating: (i) artificial soil amended with soil rinse (filter-sterilized and unfiltered) at 30°C; (ii) unfiltered soil rinse (50 ml) treated with cycloheximide (200 μg ml ), vancomycin (40 μg ml ), heat (80°C, 15 min) and no treatment (control) for 7 days at 30°C and (iii) filtered soil rinse with selected soil bacterial isolates over 7 days. There was a significant difference (P = 0·027) in E. coli O157:H7 counts after 35 days between artificial soils amended with filtered (4·45 ± 0·29) and non-filtered (1·83 ± 0·33) soil rinse. There were significant differences (P < 0·05) in E. coli O157:H7 counts after 3 days of incubation between soil rinse treatments (heat (7·04 ± 0·03), cycloheximide (6·94 ± 0·05), vancomycin (4·26 ± 0·98) and control (5·00 ± 0·93)). Lastly, a significant difference (P < 0·05) in E. coli O157:H7 counts was observed after 3 days of incubation at 30°C in filtered soil rinse when incubated with Paenibacillus alvei versus other soil bacterial isolates evaluated.
CONCLUSIONS
Soil microbiota isolated from Florida sandy soil influenced E. coli O157:H7 survival. Specifically, P. alvei reduced E. coli O157:H7 by over 3 log CFU per ml after 3 days of incubation at 30°C in filtered soil rinse.
SIGNIFICANCE AND IMPACT OF THE STUDY
This research identified soil bacterial isolates that may reduce E. coli O157:H7 in the soil environment and be used in future biocontrol applications.
Topics: Antibiosis; Biological Control Agents; Colony Count, Microbial; Escherichia coli O157; Florida; Food Microbiology; Paenibacillus; Soil; Soil Microbiology
PubMed: 33583119
DOI: 10.1111/jam.15039 -
Metabolites Sep 2019Priming is a natural phenomenon that pre-conditions plants for enhanced defence against a wide range of pathogens. It represents a complementary strategy, or sustainable...
Priming is a natural phenomenon that pre-conditions plants for enhanced defence against a wide range of pathogens. It represents a complementary strategy, or sustainable alternative that can provide protection against disease. However, a comprehensive functional and mechanistic understanding of the various layers of priming events is still limited. A non-targeted metabolomics approach was used to investigate metabolic changes in plant growth-promoting rhizobacteria (PGPR)-primed seedlings infected with the anthracnose-causing fungal pathogen, , with a focus on the post-challenge primed state phase. At the 4-leaf growth stage, the plants were treated with a strain of at 10 cfu mL. Following a 24 h PGPR application, the plants were inoculated with a spore suspension (10 spores mL), and the infection monitored over time: 1, 3, 5, 7 and 9 days post-inoculation. Non-infected plants served as negative controls. Intracellular metabolites from both inoculated and non-inoculated plants were extracted with 80% methanol-water. The extracts were chromatographically and spectrometrically analysed on an ultra-high performance liquid chromatography (UHPLC) system coupled to high-definition mass spectrometry. The acquired multidimensional data were processed to create data matrices for chemometric modelling. The computed models indicated time-related metabolic perturbations that reflect primed responses to the fungal infection. Evaluation of orthogonal projection to latent structure-discriminant analysis (OPLS-DA) loading shared and unique structures (SUS)-plots uncovered the differential stronger defence responses against the fungal infection observed in primed plants. These involved enhanced levels of amino acids (tyrosine, tryptophan), phytohormones (jasmonic acid and salicylic acid conjugates, and zeatin), and defence-related components of the lipidome. Furthermore, other defence responses in both naïve and primed plants were characterised by a complex mobilisation of phenolic compounds and biosynthesis of the flavones, apigenin and luteolin and the 3-deoxyanthocyanidin phytoalexins, apigeninidin and luteolinidin, as well as some related conjugates.
PubMed: 31547091
DOI: 10.3390/metabo9100194 -
Applied and Environmental Microbiology Jul 2019Recent papers have reported dipeptides containing d-amino acids to have novel effects that cannot be observed with ll-dipeptides, and such dipeptides are expected to be...
Recent papers have reported dipeptides containing d-amino acids to have novel effects that cannot be observed with ll-dipeptides, and such dipeptides are expected to be novel functional compounds for pharmaceuticals and food additives. Although the functions of d-amino acid-containing dipeptides are gaining more attention, there are few reports on the synthetic enzymes that can accept d-amino acids as substrates, and synthetic methods for d-amino acid-containing dipeptides have not yet been constructed. Previously, we developed a chemoenzymatic system for amide synthesis that comprised enzymatic activation and a subsequent nucleophilic substitution reaction. In this study, we demonstrated the application of the system for d-amino acid-containing-dipeptide synthesis. We chose six adenylation domains as targets according to our newly constructed hypothesis, i.e., an adenylation domain located upstream from the epimerization domain may activate d-amino acid as well as l-amino acid. We successfully synthesized over 40 kinds of d-amino acid-containing dipeptides, including ld-, dl-, and dd-dipeptides, using only two adenylation domains, TycA-A from tyrocidine synthetase and BacB2-A from bacitracin synthetase. Furthermore, this study offered the possibility that the epimerization domain could be a clue to the activity of the adenylation domains toward d-amino acid. This paper provides additional information regarding d-amino acid-containing-dipeptide synthesis through the combination of enzymatic adenylation and chemical nucleophilic reaction, and this system will be a useful tool for dipeptide synthesis. Because almost all amino acids in nature are l-amino acids, the functioning of d-amino acids has received little attention. Thus, there is little information available on the activity of enzymes toward d-amino acids or synthetic methods for d-amino acid-containing dipeptides. Recently, d-amino acids and d-amino acid-containing peptides have attracted attention as novel functional compounds, and d-amino acid-activating enzymes and synthetic methods are required for the development of the d-amino acid-containing-peptide industry. This study provides additional knowledge regarding d-amino acid-activating enzymes and proposes a unique synthetic method for d-amino acid-containing peptides, including ld-, dl-, and dd-dipeptides.
Topics: Amino Acids; Bacillus licheniformis; Bacterial Proteins; Biocatalysis; Dipeptides; Paenibacillus; Peptide Synthases; Protein Domains; Substrate Specificity
PubMed: 31003981
DOI: 10.1128/AEM.00120-19 -
Biotechnology Letters Apr 2024Microbial pretreatment of lignocellulosic biomass holds significant promise for environmentally friendly biofuel production, offering an alternative to fossil fuels....
Microbial pretreatment of lignocellulosic biomass holds significant promise for environmentally friendly biofuel production, offering an alternative to fossil fuels. This study focused on the isolation and characterization of two novel delignifying bacteria, GIET1 and GIET2, to enhance cellulose accessibility by lignin degradation. Molecular characterization confirmed their genetic identities, providing valuable microbial resources for biofuel production. Our results revealed distinct preferences for temperature, pH, and incubation period for the two bacteria. Bacillus haynesii exhibited optimal performance under moderate conditions and shorter incubation period, making it suitable for rice straw and sugarcane bagasse pretreatment. In contrast, Paenibacillus alvei thrived at higher temperatures and slightly alkaline pH, requiring a longer incubation period ideal for corn stalk pretreatment. These strain-specific requirements highlight the importance of tailoring pretreatment conditions to specific feedstocks. Structural, chemical, and morphological analyses demonstrated that microbial pretreatment reduced the amorphous lignin, increasing cellulose crystallinity and accessibility. These findings underscore the potential of microbial pretreatment to enhance biofuel production by modifying the lignocellulosic biomass. Such environmentally friendly bioconversion processes offer sustainable and cleaner energy solutions. Further research to optimize these methods for scalability and broader application is necessary in the pursuit for more efficient and greener biofuel production.
Topics: Lignin; Cellulose; Biomass; Biofuels; Saccharum; Hydrolysis
PubMed: 38252364
DOI: 10.1007/s10529-023-03463-y -
Journal of the American Society For... Oct 2015The rise of antimicrobial resistance necessitates the discovery and/or production of novel antibiotics. Isolated strains of Paenibacillus alvei were previously shown to...
The rise of antimicrobial resistance necessitates the discovery and/or production of novel antibiotics. Isolated strains of Paenibacillus alvei were previously shown to exhibit antimicrobial activity against a number of pathogens, such as E. coli, Salmonella, and methicillin-resistant Staphylococcus aureus (MRSA). The responsible antimicrobial compounds were isolated from these Paenibacillus strains and a combination of low and high resolution mass spectrometry with multiple-stage tandem mass spectrometry was used for identification. A group of closely related cyclic lipopeptides was identified, differing primarily by fatty acid chain length and one of two possible amino acid substitutions. Variation in the fatty acid length resulted in mass differences of 14 Da and yielded groups of related MS(n) spectra. Despite the inherent complexity of MS/MS spectra of cyclic compounds, straightforward analysis of these spectra was accomplished by determining differences in complementary product ion series between compounds that differ in molecular weight by 14 Da. The primary peptide sequence assignment was confirmed through genome mining; the combination of these analytical tools represents a workflow that can be used for the identification of complex antibiotics. The compounds also share amino acid sequence similarity to a previously identified broad-spectrum antibiotic isolated from Paenibacillus. The presence of such a wide distribution of related compounds produced by the same organism represents a novel class of broad-spectrum antibiotic compounds.
Topics: Amino Acid Sequence; Anti-Bacterial Agents; Escherichia coli; Methicillin-Resistant Staphylococcus aureus; Molecular Sequence Data; Paenibacillus; Peptides, Cyclic; Tandem Mass Spectrometry
PubMed: 26250559
DOI: 10.1007/s13361-015-1190-2 -
International Journal of... 2022The role of multi-heavy metal tolerant bacteria isolated from the rhizosphere of in the phytoremediation of Cu and Pb under laboratory conditions was investigated. The...
The role of multi-heavy metal tolerant bacteria isolated from the rhizosphere of in the phytoremediation of Cu and Pb under laboratory conditions was investigated. The heavy metal tolerant rhizosphere bacteria were identified as , , , , and Results showed a significant variation in wet weight, Heterotrophic Plate Count (HPC) of the rhizosphere, HPC of water, removal and uptake of Cu and Pb by , either alone or in association with the rhizosphere bacteria. The removal of Cu by in different experimental conditions showed that OTC (Oxytetracycline) untreated with rhizosphere bacteria has maximum removal with 95%, followed by alone with 84%. The OTC treated with rhizosphere bacteria could remove 81% of Cu. The maximum Pb removal efficiency of 93.4% was shown by OTC untreated with rhizosphere bacteria, followed by alone with 86.8%. The OTC treated with rhizosphere bacteria showed the least removal efficiency with 82.32%. The translocation factor (TF) values for Cu and Pb were lower than 1 indicated that the absorption was mainly accomplished in the roots of . The order of accumulation of Cu and Pb in was noted as root > leaf > petiole.
Topics: Bacteria; Biodegradation, Environmental; Eichhornia; Lead; Metals, Heavy; Rhizosphere; Water Pollutants, Chemical
PubMed: 34846266
DOI: 10.1080/15226514.2021.2007215 -
Advanced Science (Weinheim,... Feb 2024Post-translational prenylations, found in eukaryotic primary metabolites and bacterial secondary metabolites, play crucial roles in biomolecular interactions. Employing...
Post-translational prenylations, found in eukaryotic primary metabolites and bacterial secondary metabolites, play crucial roles in biomolecular interactions. Employing genome mining methods combined with AlphaFold2-based predictions of protein interactions, PalQ , a prenyltransferase responsible for the tryptophan prenylation of RiPPs produced by Paenibacillus alvei, is identified. PalQ differs from cyanobactin prenyltransferases because of its evolutionary relationship to isoprene synthases, which enables PalQ to transfer extended prenyl chains to the indole C3 position. This prenylation introduces structural diversity to the tryptophan side chain and also leads to conformational dynamics in the peptide backbone, attributed to the cis/trans isomerization that arises from the formation of a pyrrolidine ring. Additionally, PalQ exhibited pronounced positional selectivity for the C-terminal tryptophan. Such enzymatic characteristics offer a toolkit for peptide therapeutic lipidation.
Topics: Dimethylallyltranstransferase; Tryptophan; Prenylation; Protein Processing, Post-Translational; Peptides
PubMed: 38059776
DOI: 10.1002/advs.202307372 -
The Science of the Total Environment Dec 2020The pesticides belonging the strobilurin group are among the most common contaminants in the environment. In this work, biodegradation studies of the strobilurin...
The pesticides belonging the strobilurin group are among the most common contaminants in the environment. In this work, biodegradation studies of the strobilurin fungicide Pyraclostrobin by bacteria from orange cultivation plots were performed aiming to contribute with the development of a bioremediation method. Experiments were performed in triplicate with validated methods, and optimization was performed by Central Composite Design and Response Surface Methodology. The strains were evaluated in liquid nutrient medium containing 100 mg L of Pyraclostrobin, and decreased concentrations of 61.5 to 100.5 mg L were determined after 5 days at 37 °C and 130 rpm, showing the importance of strain selection. When the five most efficient strains (Bacillus sp. CSA-13, Paenibacillus alvei CBMAI2221, Bacillus sp. CBMAI2222, Bacillus safensis CBMAI2220 and Bacillus aryabhattai CBMAI2223) were used in consortia, synergistic and antagonistic effects were observed accordingly to the employed combination of bacteria, resulting in 64.2 ± 3.9 to 95.4 ± 4.9 mg L residual Pyraclostrobin. In addition, the formation of 1-(4-chlorophenyl)-1H-pyrazol-3-ol was quantified (0.59-0.01 mg L), and a new biodegradation pathway was proposed with 15 identified metabolites. Experiments were also performed in soil under controlled conditions (30 °C, 0-28 days, 100 mg kg pesticide), and the native microbiome reduced the pesticide concentration to 70.4 ± 2.3 mg L, whereas the inoculation of an efficient bacterial consortium promoted clearly better results, 57.2 ± 3.9 mg L residual Pyraclostrobin. This suggests that the introduction of these strains in soil in a bioaugmentation process increases decontamination. However, the native microbiome is important for a more efficient bioremediation.
Topics: Bacillus; Bacteria; Biodegradation, Environmental; Citrus sinensis; Fungicides, Industrial; Paenibacillus; Soil Microbiology; Soil Pollutants; Strobilurins
PubMed: 32763599
DOI: 10.1016/j.scitotenv.2020.140968 -
The Journal of Biological Chemistry Jul 2018Pro-Pro endopeptidases (PPEPs) belong to a recently discovered family of proteases capable of hydrolyzing a Pro-Pro bond. The first member from the bacterial pathogen...
Pro-Pro endopeptidases (PPEPs) belong to a recently discovered family of proteases capable of hydrolyzing a Pro-Pro bond. The first member from the bacterial pathogen (PPEP-1) cleaves two cell-surface proteins involved in adhesion, one of which is encoded by the gene adjacent to the gene. However, related PPEPs may exist in other bacteria and may shed light on substrate specificity in this enzyme family. Here, we report on the homolog of PPEP-1 in , which we denoted PPEP-2. We found that PPEP-2 is a secreted metalloprotease, which likewise cleaved a cell-surface protein encoded by an adjacent gene. However, the cleavage motif of PPEP-2, PLP↓PVP, is distinct from that of PPEP-1 (VNP↓PVP). As a result, an optimal substrate peptide for PPEP-2 was not cleaved by PPEP-1 and vice versa. To gain insight into the specificity mechanism of PPEP-2, we determined its crystal structure at 1.75 Å resolution and further confirmed the structure in solution using small-angle X-ray scattering (SAXS). We show that a four-amino-acid loop, which is distinct in PPEP-1 and -2 (GGST in PPEP-1 and SERV in PPEP-2), plays a crucial role in substrate specificity. A PPEP-2 variant, in which the four loop residues had been swapped for those from PPEP-1, displayed a shift in substrate specificity toward PPEP-1 substrates. Our results provide detailed insights into the PPEP-2 structure and the structural determinants of substrate specificity in this new family of PPEP proteases.
Topics: Amino Acid Sequence; Bacterial Proteins; Crystallography, X-Ray; Dipeptides; Endopeptidases; Models, Molecular; Paenibacillus; Protein Conformation; Sequence Homology; Substrate Specificity
PubMed: 29794027
DOI: 10.1074/jbc.RA118.003244 -
Microorganisms Aug 2023Honey bees coexist with fungi that colonize hive surfaces and pollen. Some of these fungi are opportunistic pathogens, but many are beneficial species that produce...
Honey bees coexist with fungi that colonize hive surfaces and pollen. Some of these fungi are opportunistic pathogens, but many are beneficial species that produce antimicrobial compounds for pollen conservation and the regulation of pathogen populations. In this study, we tested the in vitro antimicrobial activity of strains isolated from bee bread against (associated with European foulbrood disease) and three species that cause stonebrood disease. We found that methanol extracts of strains B18 and B195 inhibited the growth of at a concentration of 0.39 mg/mL. Bioactivity-guided dereplication revealed that the activity of the crude extracts correlated with the presence of diketopiperazines, a siderophore, and three unknown compounds. We propose that non-pathogenic fungi such as spp. and their metabolites in bee bread could be an important requirement to prevent disease. Agricultural practices involving the use of fungicides can disrupt the fungal community and thus negatively affect the health of bee colonies.
PubMed: 37630627
DOI: 10.3390/microorganisms11082067