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Microbial Cell Factories Mar 2022The genus Planococcus is comprised of halophilic bacteria generally reported for the production of carotenoid pigments and biosurfactants. In previous work, we showed...
BACKGROUND
The genus Planococcus is comprised of halophilic bacteria generally reported for the production of carotenoid pigments and biosurfactants. In previous work, we showed that the culturing of the orange-pigmented Planococcus sp. CP5-4 isolate increased the evaporation rate of industrial wastewater brine effluent, which we attributed to the orange pigment. This demonstrated the potential application of this bacterium for industrial brine effluent management in evaporation ponds for inland desalination plants. Here we identified a C-carotenoid biosynthetic gene cluster responsible for pigment biosynthesis in Planococcus sp. CP5-4 through isolation of mutants and genome sequencing. We further compare the core genes of the carotenoid biosynthetic gene clusters identified from different Planococcus species' genomes which grouped into gene cluster families containing BGCs linked to different carotenoid product chemotypes. Lastly, LC-MS analysis of saponified and unsaponified pigment extracts obtained from cultures of Planococcus sp. CP5-4, revealed the structure of the main (predominant) glucosylated C-carotenoid fatty acid ester produced by Planococcus sp. CP5-4.
RESULTS
Genome sequence comparisons of isolated mutant strains of Planococcus sp. CP5-4 showed deletions of 146 Kb and 3 Kb for the non-pigmented and "yellow" mutants respectively. Eight candidate genes, likely responsible for C-carotenoid biosynthesis, were identified on the wild-type genome region corresponding to the deleted segment in the non-pigmented mutant. Six of the eight candidate genes formed a biosynthetic gene cluster. A truncation of crtP was responsible for the "yellow" mutant phenotype. Genome annotation revealed that the genes encoded 4,4'-diapolycopene oxygenase (CrtNb), 4,4'- diapolycopen-4-al dehydrogenase (CrtNc), 4,4'-diapophytoene desaturase (CrtN), 4,4'- diaponeurosporene oxygenase (CrtP), glycerol acyltransferase (Agpat), family 2 glucosyl transferase 2 (Gtf2), phytoene/squalene synthase (CrtM), and cytochrome P450 hydroxylase enzymes. Carotenoid analysis showed that a glucosylated C-carotenoid fatty acid ester, methyl 5-(6-C)-glucosyl-5, 6'-dihydro-apo-4, 4'-lycopenoate was the main carotenoid compound produced by Planococcus sp. CP5-4.
CONCLUSION
We identified and characterized the carotenoid biosynthetic gene cluster and the C-carotenoid compound produced by Planococcus sp. CP5-4. Mass-spectrometry guided analysis of the saponified and unsaponified pigment extracts showed that methyl 5-glucosyl-5, 6-dihydro-apo-4, 4'-lycopenoate esterified to heptadecatrienoic acid (C). Furthermore, through phylogenetic analysis of the core carotenoid BGCs of Planococcus species we show that various C-carotenoid product chemotypes, apart from methyl 5-glucosyl-5, 6-dihydro-apo-4, 4'-lycopenoate and 5-glucosyl-4, 4-diaponeurosporen-4'-ol-4-oic acid, may be produced that could offer opportunities for a variety of applications.
Topics: Carotenoids; Multigene Family; Phylogeny; Planococcus Bacteria; South Africa
PubMed: 35305628
DOI: 10.1186/s12934-022-01752-1 -
Environmental Science and Pollution... Jul 2022Bio-mediated calcite precipitation potential for multiple heavy metal immobilization in contaminated soils at industrial, waste dump, abandoned mine, and landfill sites...
Bio-mediated calcite precipitation potential for multiple heavy metal immobilization in contaminated soils at industrial, waste dump, abandoned mine, and landfill sites is not explored yet. This study includes investigation of bio-mediated calcite precipitation for strength improvement and immobilization of heavy metals, specifically lead (Pb), zinc (Zn), and hexavalent chromium (Cr(VI)), in contaminated soils. Firstly, the toxicity resistance of bacteria against different concentrations (1000, 2000, 3000, 4000, and 5000 mg/l) of each heavy metals was investigated and observed that Pb and Cr were less toxic to Sporosarcina pasteurii than Zn. The poorly graded sand was spiked with 333-2000 mg/kg concentrations of a selected individual or mixed metal solutions, i.e., 1000 mg/kg and 2000 mg/kg individual concentrations of Pb, Zn, and Cr(VI); 500 mg/kg and 1000 mg/kg concentration of each metal in "Pb and Zn," "Pb and Cr(VI)," and "Zn and Cr(VI)" mixture of heavy metals; and 333 mg/kg and 666 mg/kg concentration of each metal in "Pb, Zn, and Cr(VI)" mixed metal concentration. Contaminated soil was biotreated with Sporosarcina pasteurii and cementation (a solution of urea and calcium chloride dihydrate) solutions for 18 days. Biocemented sand specimens were subjected to testing of hydraulic conductivity, ultrasonic pulse velocity (UPV), unconfined compressive strength (UCS), calcite content, pH, toxicity characteristic leaching procedure (TCLP), X-ray diffraction (XRD), and scanning electron microscopy (SEM). The heavy metal contaminated samples showed decrease in hydraulic conductivity and increase in UPV and UCS after biotreatment; however, the changes in engineering properties were found more moderate than clean biocemented sand. The conversion of Cr(VI) to Cr(III) followed by CrO precipitation in calcite lattice was observed. Zn was precipitated as smithsonite (ZnCO), while no Pb precipitate was identified in XRD results. TCLP leaching showed Pb and Cr immobilized proportional to calcite precipitated amount, and higher calcite amounts yielded levels within regulatory limits. Pb and Cr(VI) immobilization up to 92 % and 94 % was achieved, respectively, in contaminated biocemented sand. Zn was found completely leachable as smithsonite is only stable down to pH~5, and strongly acidic TCLP solution reversed all immobilization at natural soil pH~8-9.
Topics: Calcium Carbonate; Industrial Waste; Metals, Heavy; Sand; Soil; Soil Pollutants; Sporosarcina; Zinc
PubMed: 35253104
DOI: 10.1007/s11356-022-19551-x -
Microbial Cell Factories Oct 2021Members of the genus Planococcus have been revealed to utilize and degrade solvents such as aromatic hydrocarbons and alkanes, and likely to acquire tolerance to...
BACKGROUND
Members of the genus Planococcus have been revealed to utilize and degrade solvents such as aromatic hydrocarbons and alkanes, and likely to acquire tolerance to solvents. A yellow marine bacterium Planococcus maritimus strain iso-3 was isolated from an intertidal sediment that looked industrially polluted, from the Clyde estuary in the UK. This bacterium was found to produce a yellow acyclic carotenoid with a basic carbon 30 (C) structure, which was determined to be methyl 5-glucosyl-5,6-dihydro-4,4'-diapolycopenoate. In the present study, we tried to isolate and identify genes involved in carotenoid biosynthesis from this marine bacterium, and to produce novel or rare C-carotenoids with anti-oxidative activity in Escherichia coli by combinations of the isolated genes.
RESULTS
A carotenoid biosynthesis gene cluster was found out through sequence analysis of the P. maritimus genomic DNA. This cluster consisted of seven carotenoid biosynthesis candidate genes (orf1-7). Then, we isolated the individual genes and analyzed the functions of these genes by expressing them in E. coli. The results indicated that orf2 and orf1 encoded 4,4'-diapophytoene synthase (CrtM) and 4,4'-diapophytoene desaturase (CrtNa), respectively. Furthermore, orf4 and orf5 were revealed to code for hydroxydiaponeurosporene desaturase (CrtNb) and glucosyltransferase (GT), respectively. By utilizing these carotenoid biosynthesis genes, we produced five intermediate C-carotenoids. Their structural determination showed that two of them were novel compounds, 5-hydroxy-5,6-dihydro-4,4'-diaponeurosporene and 5-glucosyl-5,6-dihydro-4,4'-diapolycopene, and that one rare carotenoid 5-hydroxy-5,6-dihydro-4,4'-diapolycopene is included there. Moderate singlet oxygen-quenching activities were observed in the five C-carotenoids including the two novel and one rare compounds.
CONCLUSIONS
The carotenoid biosynthesis genes from P. maritimus strain iso-3, were isolated and functionally identified. Furthermore, we were able to produce two novel and one rare C-carotenoids in E. coli, followed by positive evaluations of their singlet oxygen-quenching activities.
Topics: Antioxidants; Carotenoids; Escherichia coli; Genes, Bacterial; Planococcaceae
PubMed: 34627253
DOI: 10.1186/s12934-021-01683-3 -
Journal of Dairy Science Apr 2021The growth of psychrotolerant aerobic spore-forming bacteria during refrigerated storage often results in the spoilage of fluid milk, leading to off-flavors and...
The growth of psychrotolerant aerobic spore-forming bacteria during refrigerated storage often results in the spoilage of fluid milk, leading to off-flavors and curdling. Because of their low toxicity, biodegradability, selectivity, and antimicrobial activity over a range of conditions, glycolipids are a novel and promising intervention to control undesirable microbes. The objective of this study was to determine the efficacy of a commercial glycolipid product to inhibit spore germination, spore outgrowth, and the growth of vegetative cells of Paenibacillus odorifer, Bacillus weihenstephanensis, and Viridibacillus arenosi, which are the predominant spore-forming spoilage bacteria in milk. For spore germination and outgrowth assays, varying concentrations (25-400 mg/L) of the glycolipid product were added to commercial UHT whole and skim milk inoculated with ∼4 log spores/mL of each bacteria and incubated at 30°C for 5 d. Inhibition of spore germination in inoculated UHT whole milk was only observed for V. arenosi, and only when glycolipid was added at 400 mg/L. However, concentrations of 400 and 200 mg/L markedly inhibited the outgrowth of vegetative cells from spores of P. odorifer and B. weihenstephanensis, respectively. No inhibition of spore germination or outgrowth was observed in inoculated UHT skim milk for any strain at the concentrations tested (25 and 50 mg/L). The effect of glycolipid addition on vegetative cell growth in UHT whole and skim milk when inoculated with ∼4 log cfu/mL of each bacteria was also determined over 21 d of storage at 7°C. Glycolipid addition at 50 mg/L was bactericidal against P. odorifer and B. weihenstephanensis in inoculated UHT skim milk through 21 d of storage, whereas 100 mg/L was needed for similar control of V. arenosi. Concentrations of 100 and 200 mg/L inhibited the growth of vegetative cells of B. weihenstephanensis and P. odorifer, respectively, in inoculated UHT whole milk, whereas 200 mg/L was also bactericidal to B. weihenstephanensis. Additional studies are necessary to identify effective concentrations for the inhibition of Viridibacillus spp. growth in whole milk beyond 7 d. Findings from this study demonstrate that natural glycolipids have the potential to inhibit the growth of dairy-spoilage bacteria and extend the shelf life of milk.
Topics: Animals; Anti-Infective Agents; Glycolipids; Milk; Paenibacillus; Planococcaceae; Spores; Spores, Bacterial
PubMed: 33589263
DOI: 10.3168/jds.2020-19769 -
Animals : An Open Access Journal From... Mar 2021Sample storage conditions are an important factor in fecal microbiota analyses in general. The objective of this study was to investigate the effect of sample storage at...
Sample storage conditions are an important factor in fecal microbiota analyses in general. The objective of this study was to investigate the effect of sample storage at room temperature on the equine fecal microbiota composition. Fecal samples were collected from 11 healthy horses. Each sample was divided into 7 sealed aliquots. One aliquot was immediately frozen at -80 °C; the remaining aliquots were stored at room temperature (21 to 22 °C) with one transferred to the freezer at each of the following time points: 6, 12, 24, 48, 72 and 96 h. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. Fibrobacteraceae () and Ruminococcaceae () were enriched in samples from 0 h and 6 h, whereas taxa from the families Bacillaceae, Planococcaceae, Enterobacteriaceae and Moraxellaceae were enriched in samples stored at room temperature for 24 h or greater. Samples frozen within the first 12 h after collection shared similar community membership. The community structure was similar for samples collected at 0 h and 6 h, but it was significantly different between samples frozen at 0 h and 12 h or greater. In conclusion, storage of equine fecal samples at ambient temperature for up to 6 h before freezing following sample collection had minimal effect on the microbial composition. Longer-term storage at ambient temperature resulted in alterations in alpha-diversity, community membership and structure and the enrichment of different taxa when compared to fecal samples immediately frozen at -80 °C.
PubMed: 33803934
DOI: 10.3390/ani11030819 -
Environmental Microbiology Aug 2011Metabolic activity, but not growth, has been observed in ice at temperatures from -5°C to -32°C. To improve understanding of metabolism in ice, we simultaneously...
Metabolic activity, but not growth, has been observed in ice at temperatures from -5°C to -32°C. To improve understanding of metabolism in ice, we simultaneously examined various aspects of metabolism ((14) C-acetate utilization, macromolecule syntheses and viability via reduction of CTC) of the glacial isolates Sporosarcina sp. B5 and Chryseobacterium sp. V3519-10 during incubation in nutrient-rich ice and brine at -5°C for 50 days. Measured rates of acetate utilization and macromolecule syntheses were high in the first 20 days suggesting adjustment to the lower temperatures and higher salt concentrations of both the liquid vein network in the ice and the brine. Following this adjustment, reproductive growth of both organisms was evident in brine, and suggested for Sporosarcina sp. B5 in ice by increases in cell numbers and biomass. Chryseobacterium sp. V3519-10 cells incubated in ice remained active. These data indicate that neither low temperature nor high salt concentrations prohibit growth in ice, but some other aspect of living within ice slows growth to within the detection limits of current methodologies. These results imply that microbial growth is plausible in natural ice systems with comparable temperatures and sufficient nutrients, such as debris-rich basal ices of glaciers and ice masses.
Topics: Acetates; Carbon Isotopes; Chryseobacterium; Cold Temperature; DNA; Ice Cover; Microbial Viability; Protein Biosynthesis; RNA; Salts; Seawater; Sporosarcina
PubMed: 21535342
DOI: 10.1111/j.1462-2920.2011.02485.x -
Bioorganic Chemistry Feb 2019Urease is a bacterial enzyme that is responsible for virulence of various pathogenic bacteria such as Staphylococcus aureus, Proteus mirabilis, Klebsiella pneumoniae,...
Urease is a bacterial enzyme that is responsible for virulence of various pathogenic bacteria such as Staphylococcus aureus, Proteus mirabilis, Klebsiella pneumoniae, Ureaplasma urealyticum, Helicobacter pylori and Mycobacterium tuberculosis. Increased urease activity aids in survival and colonization of pathogenic bacteria causing several disorders especially gastric ulceration. Hence, urease inhibitors are used for treatment of such diseases. In search of new molecules with better urease inhibitory activity, herein we report a series of acridine derived (thio)semicarbazones (4a-4e, 6a-6l) that were found to be active against urease enzyme. Molecular docking studies were carried out to better comprehend the preferential mode of binding of these compounds against urease enzyme. Docking against urease from pathogenic bacterium S. pasteurii was also carried out with favorable results. In silico ADME evaluation was done to determine drug likeness of synthesized compounds.
Topics: Acridines; Anti-Bacterial Agents; Catalytic Domain; Enzyme Inhibitors; Hydrazones; Molecular Docking Simulation; Molecular Structure; Semicarbazones; Sporosarcina; Structure-Activity Relationship; Urease
PubMed: 30267972
DOI: 10.1016/j.bioorg.2018.09.032 -
Journal of Biotechnology May 2022The microbiologically induced calcite precipitation (MICP) can be an emerging approach that could tap onto soil bacterial diversity and use as a bioremediation...
The microbiologically induced calcite precipitation (MICP) can be an emerging approach that could tap onto soil bacterial diversity and use as a bioremediation technique. Based on the concept that bacteria with biomineralization capacity could be effective CaCO inductance agents, this study aimed to evaluate the simultaneous influence of 11 operational and environmental factors on the MICP process, for the first time. Therefore, Bacillus muralis, B. lentus, B. simplex, B. firmus, and B. licheniformis, isolated from alkaline soils, were used in the selection of the best performing bacterium compared with a well-known MICP bioagent Sporosarcina pasteurii DSM 33. Plackett-Burman's experimental design was labouring to screen all independent variables for their significances on five outputs (pH value, number of viable cells and spores, amount of urea and CaCO precipitate). According to experimentally obtained data, an artificial neural network model based on the Broyden-Fletcher-Goldfarb-Shanno algorithm showed good prediction capabilities, while differences in the relative influences were observed at the bacterial strain level. B. licheniformis turn out to be the most potent bioagent, with a maximum amount of CaCO precipitate of 3.14 g/100 mL in the optimal conditions.
Topics: Bacillus; Bacteria; Biomineralization; Calcium Carbonate; Chemical Precipitation; Soil; Sporosarcina
PubMed: 35427694
DOI: 10.1016/j.jbiotec.2022.04.002 -
Journal of Applied Microbiology Dec 2022Decomposition, a complicated process, depends on several factors, including carrion insects, bacteria and the environment. However, the composition of and variation in...
AIMS
Decomposition, a complicated process, depends on several factors, including carrion insects, bacteria and the environment. However, the composition of and variation in oral bacteria over long periods of decomposition remain unclear. The current study aims to illustrate the composition of oral bacteria and construct an informative model for estimating the post-mortem interval (PMI) during decomposition.
METHODS AND RESULTS
Samples were collected from rats' oral cavities for 59 days, and 12 time points in the PMI were selected to detect bacterial community structure by sequencing the V3-V4 region of the bacterial 16S ribosomal RNA (16S rRNA) gene on the Ion S5 XL platform. The results indicated that microorganisms in the oral cavity underwent great changes during decomposition, with a tendency for variation to first decrease and then increase at day 24. Additionally, to predict the PMI, an informative model was established using the random forest algorithm. Three genera of bacteria (Atopostipes, Facklamia and Cerasibacillus) were linearly correlated at all 12 time points in the 59-day period. Planococcaceae was selected as the best feature for the last 6 time points. The R of the model reached 93.94%, which suggested high predictive accuracy. Furthermore, to predict the functions of the oral microbiota, PICRUSt results showed that energy metabolism was increased on day 3 post-mortem and carbohydrate metabolism surged significantly on days 3 and 24 post-mortem.
CONCLUSIONS
Overall, our results suggested that post-mortem oral microbial community data can serve as a forensic resource to estimate the PMI over long time periods.
SIGNIFICANCE AND IMPACT OF THE STUDY
The results of the present study are beneficial for estimating the PMI. Identifying changes in the bacterial community is of great significance for further understanding the applicability of oral flora in forensic medicine.
Topics: Rats; Animals; RNA, Ribosomal, 16S; Postmortem Changes; Microbiota; Bacteria; Mouth
PubMed: 35950442
DOI: 10.1111/jam.15771 -
Scientific Reports Mar 2021Due to their antimicrobial properties, silver nanoparticles (AgNPs) are used in a wide range of consumer products that includes topical wound dressings, coatings for...
Due to their antimicrobial properties, silver nanoparticles (AgNPs) are used in a wide range of consumer products that includes topical wound dressings, coatings for biomedical devices, and food-packaging to extend the shelf-life. Despite their beneficial antimicrobial effects, developmental exposure to such AgNPs may lead to gut dysbiosis and long-term health consequences in exposed offspring. AgNPs can cross the placenta and blood-brain-barrier to translocate in the brain of offspring. The underlying hypothesis tested in the current study was that developmental exposure of male and female mice to AgNPs disrupts the microbiome-gut-brain axis. To examine for such effects, C57BL6 female mice were exposed orally to AgNPs at a dose of 3 mg/kg BW or vehicle control 2 weeks prior to breeding and throughout gestation. Male and female offspring were tested in various mazes that measure different behavioral domains, and the gut microbial profiles were surveyed from 30 through 120 days of age. Our study results suggest that developmental exposure results in increased likelihood of engaging in repetitive behaviors and reductions in resident microglial cells. Echo-MRI results indicate increased body fat in offspring exposed to AgNPs exhibit. Coprobacillus spp., Mucispirillum spp., and Bifidobacterium spp. were reduced, while Prevotella spp., Bacillus spp., Planococcaceae, Staphylococcus spp., Enterococcus spp., and Ruminococcus spp. were increased in those developmentally exposed to NPs. These bacterial changes were linked to behavioral and metabolic alterations. In conclusion, developmental exposure of AgNPs results in long term gut dysbiosis, body fat increase and neurobehavioral alterations in offspring.
Topics: Animals; Behavior; Dysbiosis; Female; Gastrointestinal Microbiome; Humans; Male; Maze Learning; Mental Status and Dementia Tests; Metagenome; Metagenomics; Metal Nanoparticles; Mice; Models, Animal; Silver
PubMed: 33753813
DOI: 10.1038/s41598-021-85919-7