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Astrobiology Nov 2019Extraterrestrial environments encompass physicochemical conditions and habitats that are unknown on Earth, such as perchlorate-rich brines that can be at least...
Extraterrestrial environments encompass physicochemical conditions and habitats that are unknown on Earth, such as perchlorate-rich brines that can be at least temporarily stable on the martian surface. To better understand the potential for life in these cold briny environments, we determined the maximum salt concentrations suitable for growth (MSCg) of six different chloride and perchlorate salts at 25°C and 4°C for the extremotolerant cold- and salt-adapted bacterial strain . Growth was measured through colony-forming unit (CFU) counts, while cellular and colonial phenotypic stress responses were observed through visible light, fluorescence, and scanning electron microscopy. Our data show the following: (1) The tolerance to high salt concentrations can be increased through a stepwise inoculation toward higher concentrations. (2) Ion-specific factors are more relevant for the growth limitation of in saline solutions than single physicochemical parameters like ionic strength or water activity. (3) shows the highest microbial sodium perchlorate tolerance described so far. However, (4) MSCg values are higher for all chlorides compared to perchlorates. (5) The MSCg for calcium chloride was increased by lowering the temperature from 25°C to 4°C, while sodium- and magnesium-containing salts can be tolerated at 25°C to higher concentrations than at 4°C. (6) Depending on salt type and concentration, cells show distinct phenotypic stress responses such as novel types of colony morphology on agar plates and biofilm-like cell clustering, encrustation, and development of intercellular nanofilaments. This study, taken in context with previous work on the survival of extremophiles in Mars-like environments, suggests that high-concentrated perchlorate brines on Mars might not be habitable to any present organism on Earth, but extremophilic microorganisms might be able to evolve thriving in such environments.
Topics: Chlorides; Cold Temperature; Cold-Shock Response; Extraterrestrial Environment; Extreme Environments; Extremophiles; Mars; Osmolar Concentration; Perchlorates; Planococcaceae; Salt Stress; Salts
PubMed: 31386567
DOI: 10.1089/ast.2019.2069 -
Journal of Microbiology and... Aug 2012A novel two-phase anaerobic treatment technology was developed to treat high-concentration organic cassava bioethanol wastewater. The start-up process and contribution...
A novel two-phase anaerobic treatment technology was developed to treat high-concentration organic cassava bioethanol wastewater. The start-up process and contribution of organics (COD, total nitrogen, and NH4 +-N) removal in spatial succession of the whole process and spatial microbial diversity changing when sampling were analyzed. The results of the start-up phase showed that the organic loading rate could reach up to 10 kg COD/m(3)d, with the COD removal rate remaining over 90% after 25 days. The sample results indicated that the contribution of COD removal in the pre-anaerobic and anaerobic phases was 40% and 60%, respectively, with the highest efficiency of 98.5%; TN and NH4 +-N had decreased to 0.05 g/l and 0.90 g/l, respectively, and the mineralization rate of total nitrogen was 94.8%, 76.56% of which was attributed to the anaerobic part. The microbial diversity changed remarkably among different sample points depending on the physiological characteristics of identified strains. Moraxellaceae, Planococcaceae, and Prevotellaceae were dominant in the pre-anaerobic phase and Bacteroidetes, Campylobacterales, Acinetobacter, Lactobacillus, Clostridium, and Bacillus for the anaerobic phase. Methanosarcinaceae and Methanosaeta were the two main phylotypes in the anaerobic reactor.
Topics: Bacteria, Anaerobic; Biodiversity; Biological Oxygen Demand Analysis; Bioreactors; Biotechnology; Ethanol; Manihot; Nitrogen; Quaternary Ammonium Compounds
PubMed: 22713993
DOI: 10.4014/jmb.1202.02015 -
Scientific Reports Jul 2017A growing body of literature on intrinsically disordered proteins (IDPs) led scientists to rethink the structure-function paradigm of protein folding. Enzymes are often...
A growing body of literature on intrinsically disordered proteins (IDPs) led scientists to rethink the structure-function paradigm of protein folding. Enzymes are often considered an exception to the rule of intrinsic disorder (ID), believed to require a unique structure for catalysis. However, recent studies revealed the presence of disorder in several functional native enzymes. In the present work, we address the importance of dynamics for catalysis, by investigating the relationship between folding and activity in Sporosarcina pasteurii UreG (SpUreG), a P-loop GTPase and the first discovered native ID enzyme, involved in the maturation of the nickel-containing urease. The effect of denaturants and osmolytes on protein structure and activity was analyzed using circular dichroism (CD), Site-Directed Spin Labeling (SDSL) coupled to EPR spectroscopy, and enzymatic assays. Our data show that SpUreG needs a "flexibility window" to be catalytically competent, with both too low and too high mobility being detrimental for its activity.
Topics: Bacterial Proteins; Carrier Proteins; Electron Spin Resonance Spectroscopy; GTP Phosphohydrolases; Intrinsically Disordered Proteins; Models, Molecular; Phosphate-Binding Proteins; Protein Conformation; Protein Denaturation; Protein Folding; Spin Labels; Sporosarcina; Temperature
PubMed: 28729736
DOI: 10.1038/s41598-017-06330-9 -
Microorganisms Dec 2023In an attempt to isolate new probiotic bacteria, two Gram-variable, spore-forming, rod-shaped aerobic bacteria designated as strain A4 and A15 were isolated from the...
In an attempt to isolate new probiotic bacteria, two Gram-variable, spore-forming, rod-shaped aerobic bacteria designated as strain A4 and A15 were isolated from the feces of Canada geese (). Strain A4 was able to grow in high salt levels and exhibited lipase activity, while A15 did not propagate under these conditions. Both were positive for starch hydrolysis, and they inhibited the growth of . The strains of the 16S rRNA sequence shared only 94% similarity to previously identified spp. The ANI (78.08%) and AAI (82.35%) between the two strains were less than the species threshold. Searches for the most similar genomes using the Mash/Minhash algorithm showed the nearest genome to strain A4 and A15 as sp. P13 (distance of 21%) and (distance of 17%), respectively. spp. strains A4 and A15 contain urease genes, and a fibronectin-binding protein gene indicates that these bacteria may bind to eukaryotic cells in host gastrointestinal tracts. Phenotypic and phylogenetic data, along with low dDDH, ANI, and AAI values for strains A4 and A15, indicate these bacteria are two novel isolates of the genus: sp. A4 sp. nov., type strain as and sp. A15 sp. nov., type strain .
PubMed: 38257897
DOI: 10.3390/microorganisms12010070 -
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 -
Marine Drugs Mar 2021With the widespread occurrence of aquaculture diseases and the broad application of antibiotics, drug-resistant pathogens have increasingly affected aquatic animals'...
With the widespread occurrence of aquaculture diseases and the broad application of antibiotics, drug-resistant pathogens have increasingly affected aquatic animals' health. Marine probiotics, which live under high pressure in a saltwater environment, show high potential as a substitute for antibiotics in the field of aquatic disease control. In this study, twenty strains of non-hemolytic bacteria were isolated from the intestine of wild oysters and perch, and a model of infected by was established. Based on the model, ML1206, which showed a 99% similarity of 16S rRNA sequence to , was selected as a potential marine probiotic, with strong antibacterial capabilities and great acid and bile salt tolerance, to protect from being damaged by . Combined with plate counting and transmission electron microscopy, it was found that strain ML1206 could significantly inhibit colonization in the intestinal tract of . Acute oral toxicity tests in mice showed that ML1206 was safe and non-toxic. The real-time qPCR results showed a higher expression level of genes related to the antibacterial peptide () and detoxification (, , and ) in the group of protected by ML1206 compared to the control group. It is speculated that ML1206, as a potential probiotic, may inhibit the infection caused by through stimulating to secrete antibacterial effectors and detoxification proteins. This paper provides a new direction for screening marine probiotics and an experimental basis to support the potential application of ML1206 as a marine probiotic in aquaculture.
Topics: Animals; Aquaculture; Caenorhabditis elegans; Female; Intestines; Male; Mice; Mice, Inbred ICR; Ostreidae; Planococcaceae; Probiotics; RNA, Ribosomal, 16S; Survival; Vibrio; Vibrio Infections
PubMed: 33809116
DOI: 10.3390/md19030150 -
Genes Jun 2021Biogeochemical cycling of phosphorus in the agro-ecosystem is mediated by soil microbes. These microbes regulate the availability of phosphorus in the soil. Little is...
Biogeochemical cycling of phosphorus in the agro-ecosystem is mediated by soil microbes. These microbes regulate the availability of phosphorus in the soil. Little is known about the response of functional traits of phosphorus cycling microbes in soil fertilized with compost manure (derived from domestic waste and plant materials) or inorganic nitrogen fertilizers at high and low doses. We used a metagenomics investigation study to understand the changes in the abundance and distribution of microbial phosphorus cycling genes in agricultural farmlands receiving inorganic fertilizers (120 kg N/ha, 60 kg N/ha) or compost manure (8 tons/ha, 4 tons/ha), and in comparison with the control. Soil fertilization with high level of compost (Cp8) or low level of inorganic nitrogen (N1) fertilizer have nearly similar effects on the rhizosphere of maize plants in promoting the abundance of genes involved in phosphorus cycle. Genes such as involved in polyphosphate formation and (for phosphate transportation) are highly enriched in these treatments. These genes facilitate phosphorus immobilization. At a high dose of inorganic fertilizer application or low compost manure treatment, the phosphorus cycling genes were repressed and the abundance decreased. The bacterial families and were very abundant in the high inorganic fertilizer (N2) treated soil, while , , , , , , were most abundant in Cp8. , , and fungi were observed to be dominant in Cp8 and , , , and archaea have the highest percentage occurrence in Cp8. Moreover, N2 treatment, , and were most abundant among fertilized soils. Our findings have brought to light the basis for the manipulation of rhizosphere microbial communities and their genes to improve availability of phosphorus as well as phosphorus cycle regulation in agro-ecosystems.
Topics: Agriculture; Bacteria; Bacterial Proteins; Fertilizers; Manure; Metagenomics; Nitrogen; Phosphorus; Rhizosphere; Soil; Soil Microbiology; Zea mays
PubMed: 34209356
DOI: 10.3390/genes12071022 -
Frontiers in Microbiology 2019Psoriasis is a chronic inflammatory skin disease, whose pathogenesis involves dysregulated interplay among immune cells, keratinocytes and environmental triggers,...
Psoriasis is a chronic inflammatory skin disease, whose pathogenesis involves dysregulated interplay among immune cells, keratinocytes and environmental triggers, including microbiota. Bacterial and fungal dysbiosis has been recently associated with several chronic immune-mediated diseases including psoriasis. In this comprehensive study, we investigated how different sampling sites and methods reflect the uncovered skin microbiota composition. After establishing the most suitable approach, we further examined correlations between bacteria and fungi on the psoriatic skin. We compared microbiota composition determined in the same sample by sequencing two distinct hypervariable regions of the 16S rRNA gene. We showed that using the V3V4 region led to higher species richness and evenness than using the V1V2 region. In particular, genera, such as and were more abundant when using the V3V4 region, while , on the other hand, were detected only by the V1V2 region. We performed a detailed analysis of skin microbiota composition of psoriatic lesions, unaffected psoriatic skin, and healthy control skin from the back and elbow. Only a few discriminative features were uncovered, mostly specific for the sampling site or method (swab, scraping, or biopsy). Swabs from psoriatic lesions on the back and the elbow were associated with increased abundance of and and , respectively. In the same samples from psoriatic lesions, we found a significantly higher abundance of the fungus on the back, while dominated the elbow mycobiota. In psoriatic elbow skin, we found significant correlation between occurrence of , , and with , which was not observed in healthy skin. For the first time, we showed here a psoriasis-specific correlation between fungal and bacterial species, suggesting a link between competition for niche occupancy and psoriasis. However, it still remains to be elucidated whether observed microbial shift and specific inter-kingdom relationship pattern are of primary etiological significance or secondary to the disease.
PubMed: 30949136
DOI: 10.3389/fmicb.2019.00438 -
Ecotoxicology and Environmental Safety Dec 2021Serious hexavalent chromium [Cr(VI)] pollution has continuously threatened ecological security and public health. Microorganism-assisted remediation technology has...
Serious hexavalent chromium [Cr(VI)] pollution has continuously threatened ecological security and public health. Microorganism-assisted remediation technology has strong potential in the treatment of environmental Cr(VI) pollution due to its advantages of high efficiency, low cost, and low secondary pollution. Sporosarcina saromensis M52, a strain with strong Cr(VI) removal ability, isolated from coastal intertidal zone was used in this study. Scanning electron microscopy coupled with energy dispersive X-ray analysis indicated M52 was relatively stable under Cr(VI) stress and trace amount of Cr deposited on the cell surface. X-ray photoelectron spectroscopy and X-ray diffraction analyses exhibited M52 could reduce Cr(VI) into Cr(III). Fourier transform infrared spectroscopy showed the bacterial surface was mainly consisted of polysaccharides, phosphate groups, carboxyl groups, amide II (NH/CN) groups, alkyl groups, and hydroxyl groups, while functional groups involving in Cr(VI) bio-reduction were not detected. According to these characterization analyses, the removal of Cr(VI) was primarily depended on bio-reduction, instead of bio-adsorption by M52. Genome analyses further indicated the probable mechanisms of bio-reduction, including the active efflux of Cr(VI) by chromate transporter ChrA, enzymatic redox reactions mediated by reductases, DNA-repaired proteases ability to minimize the ROS damage, and the formation of specific cell components to minimize the biofilm injuries caused by Cr(VI). These studies provided a theoretical basis which was useful for Cr(VI) remediation, especially in terms of increasing its effectiveness. THE MAIN FINDING OF THE WORK: M52 realized the bioremediation of Cr(VI) majorly through bio-reduction, including Cr(VI) efflux, chromate reduction, DNA repair, and the formation of specific cell components, instead of bio-adsorption.
Topics: Chromium; Genomics; Sporosarcina
PubMed: 34507039
DOI: 10.1016/j.ecoenv.2021.112767 -
Microbiology Spectrum Dec 2023Since 1988, through the United States government's founding, the National Center for Biotechnology Information (NCBI) has provided an invaluable service to scientific...
Since 1988, through the United States government's founding, the National Center for Biotechnology Information (NCBI) has provided an invaluable service to scientific advancement. The universality and total freedom of use if on the one hand allow the use of this database on a global level by all researchers for their valuable work, on the other hand, it has the disadvantage of making it difficult to check the correctness of all the materials present. It is, therefore, of fundamental importance for the correctness and ethics of research to improve the databases at our disposal, identifying and amending the critical issues. This work aims to provide the scientific community with a new sequence for the type strain SK 55 and broaden the knowledge of the species, in particular, considering the ancient strain Aquil_B6 found in an ancient Roman amphora.
Topics: United States; DNA, Bacterial; Bacillaceae; Planococcaceae
PubMed: 37975675
DOI: 10.1128/spectrum.00686-23