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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 -
PloS One 2019Microbially induced calcium carbonate precipitation (MICP) is a potential method for improvement of soil. A laboratory study was conducted to investigate the influence...
Microbially induced calcium carbonate precipitation (MICP) is a potential method for improvement of soil. A laboratory study was conducted to investigate the influence of temperatures for soil improvement by MICP. The ureolytic activity experiments, MICP experiments in aqueous solution and sand column using Sporosarcina pasteurii were conducted at different temperatures(10, 15, 20, 25 and 30°C). The results showed there were microbially induced CaCO3 precipitation at all the temperatures from 10 to 30°C. The results of ureolytic activity experiments showed that the bacterial had higher ureolytic activity at high temperatures within the early 20 hours, however, the ureolytic activity at higher temperatures decreased more quickly than at lower temperatures. The results of MICP experiments in aqueous solution and sand column were consistent with tests of ureolytic activity. Within 20 to 50 hours of the start of the test, more CaCO3 precipitation was precipitated at higher temperature, subsequently, the precipitation rate of all experiments decreased, and the higher the temperature, the faster the precipitation rate dropped. The final precipitation amount of CaCO3 in aqueous solution and sand column tests at 10 °C was 92% and 37% higher than that at 30 °C. The maximum unconfined compressive strength of MICP treated sand column at 10 °C was 135% higher than that at 30 °C. The final treatment effect of MICP at lower temperature was better than that at high temperature within the temperature range studied. The reason for better treatment effect at lower temperatures was due to the longer retention time of ureolytic activity of bacteria at lower temperatures.
Topics: Calcium Carbonate; Chemical Precipitation; Soil Microbiology; Sporosarcina; Temperature; Urea; Water
PubMed: 31211807
DOI: 10.1371/journal.pone.0218396 -
Genomics, Proteomics & Bioinformatics Feb 2019Proton pump inhibitors (PPIs) are commonly used to lessen symptoms in patients with gastroesophageal reflux disease (GERD). However, the effects of PPI therapy on the...
Proton pump inhibitors (PPIs) are commonly used to lessen symptoms in patients with gastroesophageal reflux disease (GERD). However, the effects of PPI therapy on the gastrointestinal microbiota in GERD patients remain unclear. We examined the association between the PPI usage and the microbiota present in gastric mucosal and fecal samples from GERD patients and healthy controls (HCs) using 16S rRNA gene sequencing. GERD patients taking PPIs were further divided into short-term and long-term PPI user groups. We showed that PPI administration lowered the relative bacterial diversity of the gastric microbiota in GERD patients. Compared to the non-PPI-user and HC groups, higher abundances of Planococcaceae, Oxalobacteraceae, and Sphingomonadaceae were found in the gastric microbiota from the PPI-user group. In addition, the Methylophilus genus was more highly abundant in the long-term PPI user group than in the short-term PPI-user group. Despite the absence of differences in alpha diversity, there were significant differences in the fecal bacterial composition of between GERD patients taking PPIs and those not taking PPIs. There was a higher abundance of Streptococcaceae, Veillonellaceae, Acidaminococcaceae, Micrococcaceae, and Flavobacteriaceae present in the fecal microbiota from the PPI-user group than those from the non-PPI-user and HC groups. Additionally, a significantly higher abundance of Ruminococcus was found in GERD patients on long-term PPI medication than that on short-term PPI medication. Our study indicates that PPI administration in patients with GERD has a significant effect on the abundance and structure of the gastric mucosal microbiota but only on the composition of the fecal microbiota.
Topics: Adult; Aged; Bacteria; Feces; Female; Gastric Mucosa; Gastroesophageal Reflux; Gastrointestinal Microbiome; Humans; Male; Microbiota; Middle Aged; Proton Pump Inhibitors; RNA, Ribosomal, 16S
PubMed: 31028880
DOI: 10.1016/j.gpb.2018.12.004 -
Food Microbiology Sep 2019The Minas artisanal cheese is a traditional product in its way of producing. Produced in the Minas Gerais state, Brazil, this cheese is made using raw cow's milk with...
The Minas artisanal cheese is a traditional product in its way of producing. Produced in the Minas Gerais state, Brazil, this cheese is made using raw cow's milk with the addition of an endogenous starter culture called "pingo", responsible for inoculating specific microorganisms that could enhance flavor and sensorial aspects. There are seven regions able to produce and commercialize this product - Araxá, Campo das Vertentes, Canastra Cerrado, Serra do Salitre, Serro and Triângulo Mineiro. This study aimed to assess the bacterial community of raw milk, endogenous starter culture and to uncover possible shifts in the bacterial community of the rind and core of cheeses at sixty days of ripening located in the Serra do Salitre region by Illumina MiSeq 16S rRNA gene amplicon sequencing. Raw milk and starter culture are responsible for inoculating specific bacteria into the cheese, with Planococcaceae and Streptococcaceae being prevalent throughout ripening time. The Planococcaceae family seems to develop strong interactions with the Leuconostocaceae family on the surface of these cheeses, and is associated with environmental aspects of the region, probably leading to a microbial signature of these products. Additionally, abiotic factors such as geographical location, moisture and acidity are major drivers in the microbial shift.
Topics: Animals; Bacteria; Brazil; Cheese; Environment; Food Microbiology; Microbiota; Milk; RNA, Ribosomal, 16S; Sensation; Taste; Time Factors
PubMed: 31027793
DOI: 10.1016/j.fm.2019.02.016 -
Biochemical and Biophysical Research... May 2019In cold and harsh environments such as glaciers and sediments in ice cores, microbes can survive by forming spores. Spores are composed of a thick coat protein, which...
In cold and harsh environments such as glaciers and sediments in ice cores, microbes can survive by forming spores. Spores are composed of a thick coat protein, which protects against external factors such as heat-shock, high salinity, and nutrient deficiency. GerE is a key transcription factor involved in spore coat protein expression in the mother cell during sporulation. GerE regulates transcription during the late sporulation stage by directly binding to the promoter of cotB gene. Here, we report the crystal structure of PaGerE at 2.09 Å resolution from Paenisporosarcina sp. TG-14, which was isolated from the Taylor glacier. The PaGerE structure is composed of four α-helices and adopts a helix-turn-helix architecture with 68 amino acid residues. Based on our DNA binding analysis, the PaGerE binds to the promoter region of CotB to affect protein expression. Additionally, our structural comparison studies suggest that DNA binding by PaGerE causes a conformational change in the α4-helix region, which may strongly induce dimerization of PaGerE.
Topics: Amino Acid Sequence; Bacterial Proteins; Crystallography, X-Ray; Models, Molecular; Protein Conformation; Sequence Alignment; Sporosarcina; Transcription Factors
PubMed: 30967265
DOI: 10.1016/j.bbrc.2019.04.019 -
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 -
Acta Crystallographica. Section D,... Feb 2019Single-wavelength anomalous diffraction (SAD) phasing from multiple crystals can be especially challenging in samples with weak anomalous signals and/or strong...
Single-wavelength anomalous diffraction (SAD) phasing from multiple crystals can be especially challenging in samples with weak anomalous signals and/or strong non-isomorphism. Here, advantage is taken of the combinatorial diversity possible in such experiments to study the relationship between merging statistics and downstream metrics of phasing signals. It is furthermore shown that a genetic algorithm (GA) can be used to optimize the grouping of data sets to enhance weak anomalous signals based on these merging statistics.
Topics: Algorithms; Bacillus; Bacterial Proteins; Crystallization; Crystallography, X-Ray; Data Collection; Models, Molecular; Protein Conformation; Sporosarcina; Thermolysin; Urease
PubMed: 30821708
DOI: 10.1107/S205979831801570X -
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 -
PloS One 2018The bacterium Sporosarcina pasteurii can produce significant volumes of solid precipitation in the presence of specific chemical environments. These solid precipitate...
The bacterium Sporosarcina pasteurii can produce significant volumes of solid precipitation in the presence of specific chemical environments. These solid precipitate particles can enter a network of microscale pores and cause long-range clogging. As a result, the medium gains strength and exhibits superior mechanical properties. This concept is also known as Microbiologically Induced Calcite Precipitation (MICP). In this study, we have used sponge blocks as surrogate porous media mimics and analyzed several aspects of MICP. A synergistic approach involving electron microscopy (SEM), computerized X-Ray tomography (μCT), quasi-static compressive load testing and chemical characterization (EDX) has been used to understand several physical and chemical aspects of MICP.
Topics: Calcium Carbonate; Flocculation; Porosity; Sporosarcina
PubMed: 30500841
DOI: 10.1371/journal.pone.0207489 -
Microbial Cell Factories Nov 2018N-acylhomoserine lactones (AHLs) are well-studied signalling molecules produced by some Gram-negative Proteobacteria for bacterial cell-to-cell communication or quorum...
BACKGROUND
N-acylhomoserine lactones (AHLs) are well-studied signalling molecules produced by some Gram-negative Proteobacteria for bacterial cell-to-cell communication or quorum sensing. We have previously demonstrated the degradation of AHLs by an Antarctic bacterium, Planococcus versutus L10.15, at low temperature through the production of an AHL lactonase. In this study, we cloned the AHL lactonase gene and characterized the purified novel enzyme.
RESULTS
Rapid resolution liquid chromatography analysis indicated that purified AidP possesses high AHL-degrading activity on unsubstituted, and 3-oxo substituted homoserine lactones. Liquid chromatography-mass spectrometry analysis confirmed that AidP functions as an AHL lactonase that hydrolyzes the ester bond of the homoserine lactone ring of AHLs. Multiple sequence alignment analysis and phylogenetic analysis suggested that the aidP gene encodes a novel AHL lactonase enzyme. The amino acid composition analysis of aidP and the homologous genes suggested that it might be a cold-adapted enzyme, however, the optimum temperature is 28 °C, even though the thermal stability is low (reduced drastically above 32 °C). Branch-site analysis of several aidP genes of Planococcus sp. branch on the phylogenetic trees also showed evidence of episodic positive selection of the gene in cold environments. Furthermore, we demonstrated the effects of covalent and ionic bonding, showing that Zn is important for activity of AidP in vivo. The pectinolytic inhibition assay confirmed that this enzyme attenuated the pathogenicity of the plant pathogen Pectobacterium carotovorum in Chinese cabbage.
CONCLUSION
We demonstrated that AidP is effective in attenuating the pathogenicity of P. carotovorum, a plant pathogen that causes soft-rot disease. This anti-quorum sensing agent is an enzyme with low thermal stability that degrades the bacterial signalling molecules (AHLs) that are produced by many pathogens. Since the enzyme is most active below human body temperature (below 28 °C), and lose its activity drastically above 32 °C, the results of a pectinolytic inhibition assay using Chinese cabbage indicated the potential of this anti-quorum sensing agent to be safely applied in the field trials.
Topics: 4-Butyrolactone; Amino Acid Sequence; Antarctic Regions; Bacterial Proteins; Carboxylic Ester Hydrolases; Models, Molecular; Pectins; Pectobacterium carotovorum; Planococcus Bacteria; Quorum Sensing; Sequence Analysis, Protein; Substrate Specificity
PubMed: 30445965
DOI: 10.1186/s12934-018-1024-6