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PloS One 2019The bacterium Sporosarcina pasteurii (SP) is known for its ability to cause the phenomenon of microbially induced calcium carbonate precipitation (MICP). We explored...
The bacterium Sporosarcina pasteurii (SP) is known for its ability to cause the phenomenon of microbially induced calcium carbonate precipitation (MICP). We explored bacterial participation in the initial stages of the MICP process at the cellular length scale under two different growth environments (a) liquid culture (b) MICP in a soft agar (0.5%) column. In the liquid culture, ex-situ imaging of the cellular environment indicated that S. pasteurii was facilitating nucleation of nanoscale crystals of calcium carbonate on bacterial cell surface and its growth via ureolysis. During the same period, the meso-scale environment (bulk medium) was found to have overgrown calcium carbonate crystals. The effect of media components (urea, CaCl2), presence of live and dead in the growth medium were explored. The agar column method allows for in-situ visualization of the phenomena, and using this platform, we found conclusive evidence of the bacterial cell surface facilitating formation of nanoscale crystals in the microenvironment. Here also the bulk environment or the meso-scale environment was found to possess overgrown calcium carbonate crystals. Extensive elemental analysis using Energy dispersive X-ray spectroscopy (EDS) and X-ray powder diffraction (XRD), confirmed that the crystals to be calcium carbonate, and two different polymorphs (calcite and vaterite) were identified. Active participation of S. pasteurii cell surface as the site of calcium carbonate precipitation has been shown using EDS elemental mapping with Scanning transmission electron microscopy (STEM) and scanning electron microscopy (SEM).
Topics: Biomineralization; Calcium Carbonate; Cell Membrane; Crystallization; Culture Media; Microscopy, Electron, Scanning; Microscopy, Electron, Scanning Transmission; Nanostructures; Powder Diffraction; Spectrometry, X-Ray Emission; Sporosarcina
PubMed: 30699142
DOI: 10.1371/journal.pone.0210339 -
Scientific Reports Jan 2021Human activities interfere with wild animals and lead to the loss of many animal populations. Therefore, efforts have been made to understand how wildlife can rebound...
Human activities interfere with wild animals and lead to the loss of many animal populations. Therefore, efforts have been made to understand how wildlife can rebound from anthropogenic disturbances. An essential mechanism to adapt to environmental and social changes is the fluctuations in the host gut microbiome. Here we give a comprehensive description of anthropogenically induced microbiome alterations in Asian elephants (n = 30). We detected gut microbial changes due to overseas translocation, captivity and deworming. We found that microbes belonging to Planococcaceae had the highest contribution in the microbiome alterations after translocation, while Clostridiaceae, Spirochaetaceae and Bacteroidia were the most affected after captivity. However, deworming significantly changed the abundance of Flavobacteriaceae, Sphingobacteriaceae, Xanthomonadaceae, Weeksellaceae and Burkholderiaceae. These findings may provide fundamental ideas to help guide the preservation tactics and probiotic replacement therapies of a dysbiosed gut microbiome in Asian elephants. More generally, these results show the severity of anthropogenic activities at the level of gut microbiome, altering the adaptation processes to new environments and the subsequent capability to maintain normal physiological processes in animals.
Topics: Adaptation, Physiological; Animals; Asia; Dysbiosis; Ecosystem; Elephants; Environmental Monitoring; Female; Gastrointestinal Microbiome; Male
PubMed: 33436882
DOI: 10.1038/s41598-020-80537-1 -
Journal of Hazardous Materials Mar 2021In this study, the performances of Sporosarcina saromensis W5 assisted bio-permeable reactive barrier, containing activated carbon (AC) or zero-valent iron (ZVI), were...
In this study, the performances of Sporosarcina saromensis W5 assisted bio-permeable reactive barrier, containing activated carbon (AC) or zero-valent iron (ZVI), were investigated by column experiments in removal of Cr(Ⅵ) from simulated groundwater. The enhanced Cr(Ⅵ) removal performances were observed in biotic columns. Cr(Ⅵ) was first detected in effluent on day 24 and day 85 in Bio-AC and Bio-ZVI columns, respectively whereas it breakthrough only on day 4 and day 15 in AC and ZVI columns. Additionally, Cr(Ⅵ) removal performances induced by biofilm in Bio-QZ columns were promoted with the increase of influent Cr(Ⅵ) concentrations. According to fluorescent images, activated carbon was found to be the best biofilm carrier. Fe may not be suitable for microbial colonization because biofilm depolymerization occurred on Fe surface. Moreover, high concentration of Cr(Ⅵ) would lag the evolution of biofilm. Magnetite generating was found on the Fe surface. X-ray photoelectron spectroscopy (XPS) analysis indicated that the removal mechanism of Cr(Ⅵ) in biotic columns was biotransformation of Cr(Ⅵ) to Cr(Ш) species. Our results may provide a new insight in Cr(Ⅵ) in-situ remediation from groundwater by Bio-PRB system.
Topics: Chromium; Groundwater; Sporosarcina; Water Pollutants, Chemical
PubMed: 33535357
DOI: 10.1016/j.jhazmat.2020.124115 -
Journal of Biotechnology Nov 2022Caproic acid is the precursor of ethyl caproate, the main representative flavor substance of strong-flavor baijiu (SFB). Caproic acid-producing bacteria are considered...
Caproic acid is the precursor of ethyl caproate, the main representative flavor substance of strong-flavor baijiu (SFB). Caproic acid-producing bacteria are considered to be the most important type of acid-producing microorganisms in the pit mud of the SFB ecosystem. In this study, the Rummeliibacillus suwonensis 3B-1 with a high yield of caproic acid (4.064 g/L) was screened from SFB pit mud. The genome of the R. suwonensis 3B-1 was sequenced, the total size was found to be 4117,671 bp and a calculated GC content of 35.86%. The caproic acid biosynthesis pathway was identified and analyzed, and it showed that 3B-1 could not only use ethanol, but it could also use glucose and other carbon sources as substrates to produce caproic acid. According to the genome analysis and with an optimized medium, the optimal conditions for caproic acid production were yeast powder at 3 g/L, sodium acetate at 15 g/L, and 1% biotin at 8 mL/100 mL. The yield of caproic acid reached 4.627 g/L, an increase of 13.9%, which was higher than that of general caproic acid bacteria. This is the first report of the synthesis of caproic acid by R. suwonensis. This strain could be used to produce caproic acid, an artificial pit mud preparation, and/or an enhanced inoculum in the production of SFB.
Topics: Alcoholic Beverages; Bacteria; Biotin; Caproates; Carbon; Ecosystem; Ethanol; Fermentation; Glucose; Planococcaceae; Powders; Sodium Acetate
PubMed: 36049550
DOI: 10.1016/j.jbiotec.2022.08.017 -
Nucleic Acids Research Apr 2021Argonaute proteins are programmable nucleases that are found in both eukaryotes and prokaryotes and provide defense against invading genetic elements. Although some...
Argonaute proteins are programmable nucleases that are found in both eukaryotes and prokaryotes and provide defense against invading genetic elements. Although some prokaryotic argonautes (pAgos) were shown to recognize RNA targets in vitro, the majority of studied pAgos have strict specificity toward DNA, which limits their practical use in RNA-centric applications. Here, we describe a unique pAgo nuclease, KmAgo, from the mesophilic bacterium Kurthia massiliensis that can be programmed with either DNA or RNA guides and can precisely cleave both DNA and RNA targets. KmAgo binds 16-20 nt long 5'-phosphorylated guide molecules with no strict specificity for their sequence and is active in a wide range of temperatures. In bacterial cells, KmAgo is loaded with small DNAs with no obvious sequence preferences suggesting that it can uniformly target genomic sequences. Mismatches between the guide and target sequences greatly affect the efficiency and precision of target cleavage, depending on the mismatch position and the nature of the reacting nucleic acids. Target RNA cleavage by KmAgo depends on the formation of secondary structure indicating that KmAgo can be used for structural probing of RNA. These properties of KmAgo open the way for its use for highly specific nucleic acid detection and cleavage.
Topics: Argonaute Proteins; Bacterial Proteins; DNA, Bacterial; Planococcaceae; Protein Binding; RNA, Bacterial; Substrate Specificity
PubMed: 33744962
DOI: 10.1093/nar/gkab182 -
Scientific Reports Oct 2019We demonstrate for the first time that the morphology and nanomechanical properties of calcium carbonate (CaCO) can be tailored by modulating the precipitation kinetics...
We demonstrate for the first time that the morphology and nanomechanical properties of calcium carbonate (CaCO) can be tailored by modulating the precipitation kinetics of ureolytic microorganisms through genetic engineering. Many engineering applications employ microorganisms to produce CaCO. However, control over bacterial calcite morphology and material properties has not been demonstrated. We hypothesized that microorganisms genetically engineered for low urease activity would achieve larger calcite crystals with higher moduli. We compared precipitation kinetics, morphology, and nanomechanical properties for biogenic CaCO produced by two Escherichia coli (E. coli) strains that were engineered to display either high or low urease activity and the native producer Sporosarcina pasteurii. While all three microorganisms produced calcite, lower urease activity was associated with both slower initial calcium depletion rate and increased average calcite crystal size. Both calcite crystal size and nanoindentation moduli were also significantly higher for the low-urease activity E. coli compared with the high-urease activity E. coli. The relative resistance to inelastic deformation, measured via the ratio of nanoindentation hardness to modulus, was similar across microorganisms. These findings may enable design of novel advanced engineering materials where modulus is tailored to the application while resistance to irreversible deformation is not compromised.
Topics: Calcium Carbonate; Chemical Precipitation; Crystallization; Escherichia coli; Kinetics; Metabolic Engineering; Microscopy, Electron, Scanning; Organisms, Genetically Modified; Sporosarcina; Urease; X-Ray Diffraction
PubMed: 31604977
DOI: 10.1038/s41598-019-51133-9 -
Dalton Transactions (Cambridge, England... Oct 2021A few gold compounds were recently found to show antimicrobial properties , holding great promise for the discovery of new drugs to overcome antibiotic resistance. Here,...
A few gold compounds were recently found to show antimicrobial properties , holding great promise for the discovery of new drugs to overcome antibiotic resistance. Here, the inhibition of the bacterial virulence factor urease by four Au(I)-compounds, namely Au(PEt)Cl, Au(PEt)Br, Au(PEt)I and [Au(PEt)]Cl, obtained from the antiarthritic Au(I)-drug Auranofin and earlier reported to act as antimicrobials, is investigated. The three monophosphino Au(I) complexes showed IC values in the 30-100 nM range, while the diphosphino Au(I) complex, though being less active, still showed a IC value of 7 μM. The structural basis for this inhibition was provided by solving the crystal structures of urease co-crystallized with Au(PEt)I and [Au(PEt)]Cl: at least two Au(I) ions bind the enzyme in a flap domain involved in the catalysis, thus obliterating enzyme activity. Peculiar changes observed in the two structures reveal implications for the mechanism of soft metal binding and enzyme inactivation.
Topics: Anti-Bacterial Agents; Crystallography, X-Ray; Density Functional Theory; Enzyme Inhibitors; Microbial Sensitivity Tests; Models, Molecular; Molecular Structure; Organogold Compounds; Sporosarcina; Urease
PubMed: 34585201
DOI: 10.1039/d1dt02488d -
International Microbiology : the... Aug 2021Sabkhas in Kuwait are unique hypersaline marine environments under-explored for bacterial community composition and bioprospecting. The 16S rRNA sequence analysis of 46...
Sabkhas in Kuwait are unique hypersaline marine environments under-explored for bacterial community composition and bioprospecting. The 16S rRNA sequence analysis of 46 isolates with distinct morphology from two Kuwait sabkhas recovered 11 genera. Phylum Firmicutes dominated these isolates, and Bacillus (32.6%) was recovered as the dominant genera, followed by Halococcus (17.4%). These isolates were moderately halophilic, and some of them showed tolerance and growth at extreme levels of salt (20%), pH (5 and/or 11), and temperature (55 °C). A higher percentage of isolates harbored protease (63.0), followed by DNase (41.3), amylase (41.3), and lipase (32.6). Selected isolates showed antimicrobial activity against E. faecalis and isolated Halomonas shengliensis, and Idiomarina piscisalsi harbored gene coding for dNDP-glucose 4,6-dehydratase (Glu 1), indicating their potential to produce biomolecules with deoxysugar moieties. Palmitic acid or oleic acid was the dominant fatty acid, and seven isolates had some polyunsaturated fatty acids (linolenic or γ-linolenic acid). Interestingly, six isolates belonging to Planococcus and Oceanobacillus genus produced squalene, a bioactive isoprenoid molecule. Their content increased 30-50% in the presence of Terbinafine. The potential bioactivities and extreme growth conditions make this untapped bacterial diversity a promising candidate for future bioprospecting studies.
Topics: Anti-Infective Agents; Antineoplastic Agents; Bacillus; Bacteria; Bacterial Proteins; Biodiversity; Bioprospecting; DNA, Bacterial; Enzymes; Fatty Acids; Firmicutes; Geologic Sediments; Halococcus; Kuwait; Phylogeny; Planococcaceae; RNA, Ribosomal, 16S; Salinity; Squalene; Water Microbiology
PubMed: 33755814
DOI: 10.1007/s10123-021-00173-1 -
Acta Crystallographica. Section F,... Nov 2018The determination of conditions for the reproducible growth of well diffracting crystals is a critical step in every biocrystallographic study. On the occasion of a new...
The determination of conditions for the reproducible growth of well diffracting crystals is a critical step in every biocrystallographic study. On the occasion of a new structural biology project, several advanced crystallogenesis approaches were tested in order to increase the success rate of crystallization. These methods included screening by microseed matrix screening, optimization by counter-diffusion and crystal detection by trace fluorescent labeling, and are easily accessible to any laboratory. Their combination proved to be particularly efficient in the case of the target, a 48 kDa CCA-adding enzyme from the psychrophilic bacterium Planococcus halocryophilus. A workflow summarizes the overall strategy, which led to the production of crystals that diffracted to better than 2 Å resolution and may be of general interest for a variety of applications.
Topics: Bacterial Proteins; Crystallization; Crystallography, X-Ray; Escherichia coli; Planococcus Bacteria; RNA Nucleotidyltransferases; Recombinant Proteins; Workflow
PubMed: 30387781
DOI: 10.1107/S2053230X18014590 -
Applied Biochemistry and Biotechnology Nov 2018Novel synthetic isoprenoids have been synthesized in engineered microbial hosts by evolving terpene synthase or expressing heterologous terpene synthases. Recently, the...
Novel synthetic isoprenoids have been synthesized in engineered microbial hosts by evolving terpene synthase or expressing heterologous terpene synthases. Recently, the native operon, crtNNM derived from Planococcus sp. PAMC 21323, has isolated for potential industrial applications of C carotenoids. For the first time, novel C carotenoids (sesquarterpene) were synthesized in Corynebacterium glutamicum expressing the crtNNM genes. The recombinant strains accumulate various sesquarterpene including 4-apolycopene (red color), 4-aponeurosporene (yellow color), and no pigmentation, depending on the expression of the genetic elements of the crtNNM genes. Subsequently, the carotenoid extract from the cells harboring pCES-H36-CrtNNM was analyzed, resulting in significantly higher antioxidant activity than those of other strains harboring pCES-H36-CrtNM and pCES-H36-CrtNN, respectively. This study will promote further engineering of C. glutamicum to increase sesquarterpene productions.
Topics: Antioxidants; Carotenoids; Corynebacterium glutamicum; Genes, Bacterial; Genetic Engineering; Planococcus Bacteria; Recombination, Genetic; Sesquiterpenes
PubMed: 29663127
DOI: 10.1007/s12010-018-2756-9