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Molecules (Basel, Switzerland) Sep 2020Antarctic regions are characterized by low temperatures and strong UV radiation. This harsh environment is inhabited by psychrophilic and psychrotolerant organisms,...
Antarctic regions are characterized by low temperatures and strong UV radiation. This harsh environment is inhabited by psychrophilic and psychrotolerant organisms, which have developed several adaptive features. In this study, we analyzed two Antarctic bacterial strains, sp. ANT_H30 and sp. ANT_H53B. The physiological analysis of these strains revealed their potential to produce various biotechnologically valuable secondary metabolites, including surfactants, siderophores, and orange pigments. The genomic characterization of ANT_H30 and ANT_H53B allowed the identification of genes responsible for the production of carotenoids and the in silico reconstruction of the pigment biosynthesis pathways. The complex manual annotation of the bacterial genomes revealed the metabolic potential to degrade a wide variety of compounds, including xenobiotics and waste materials. Carotenoids produced by these bacteria were analyzed chromatographically, and we proved their activity as scavengers of free radicals. The quantity of crude carotenoid extracts produced at two temperatures using various media was also determined. This was a step toward the optimization of carotenoid production by Antarctic bacteria on a larger scale.
Topics: Carotenoids; Genome, Bacterial; Genomics; Multigene Family; Phylogeny; Planococcus Bacteria; Rhodococcus
PubMed: 32977394
DOI: 10.3390/molecules25194357 -
Journal of Biological Inorganic... Sep 2020This review is an attempt to retrace the chronicle that starts from the discovery of the role of nickel as the essential metal ion in urease for the enzymatic catalysis... (Review)
Review
This review is an attempt to retrace the chronicle that starts from the discovery of the role of nickel as the essential metal ion in urease for the enzymatic catalysis of urea, a key step in the biogeochemical cycle of nitrogen on Earth, to the most recent progress in understanding the chemistry of this historical enzyme. Data and facts are presented through the magnifying lenses of the authors, using their best judgment to filter and elaborate on the many facets of the research carried out on this metalloenzyme over the years. The tale is divided in chapters that discuss and describe the results obtained in the subsequent leaps in the knowledge that led from the discovery of a biological role for Ni to the most recent advancements in the comprehension of the relationship between the structure and function of urease. This review is intended not only to focus on the bioinorganic chemistry of this beautiful metal-based catalysis, but also, and maybe primarily, to evoke inspiration and motivation to further explore the realm of bio-based coordination chemistry.
Topics: Bacterial Proteins; Binding Sites; Catalysis; Crystallography, X-Ray; Enterobacter aerogenes; Helicobacter pylori; Nickel; Protein Conformation; Signal Transduction; Sporosarcina; Structure-Activity Relationship; Urease
PubMed: 32809087
DOI: 10.1007/s00775-020-01808-w -
Molecules (Basel, Switzerland) Jun 2020The use of bacteria as nanofactories for the green synthesis of nanoparticles is considered a sustainable approach, owing to the stability, biocompatibility, high yields...
The use of bacteria as nanofactories for the green synthesis of nanoparticles is considered a sustainable approach, owing to the stability, biocompatibility, high yields and facile synthesis of nanoparticles. The green synthesis provides the coating or capping of biomolecules on nanoparticles surface, which confer their biological activity. In this study, we report green synthesis of silver nanoparticles (AgNPs) by an environmental isolate; named as AgNPs1, which showed 100% 16S rRNA sequence similarity with UV/visible analysis (UV/Vis), transmission electron microscopy (TEM), atomic force microscopy (AFM), dynamic light scattering (DLS), and Fourier-transform infrared spectroscopy (FTIR) were used to characterize the synthesized nanoparticles. The stable nature of nanoparticles was studied by thermogravimetric analysis (TGA) and inductively coupled plasma mass spectrometry (ICP-MS). Further, these nanoparticles were tested for biofilm inhibition against and . The AgNPs showed minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values of 3.12 µg/mL and 6.25 µg/mL for , and 1.56 µg/mL and 3.12 µg/mL for , respectively.
Topics: Biofilms; Escherichia coli; Green Chemistry Technology; Metal Nanoparticles; Planococcaceae; Pseudomonas aeruginosa; Silver
PubMed: 32560208
DOI: 10.3390/molecules25122783 -
MicrobiologyOpen Jun 2020Strain Y74 was an isolate from the sandy soil in the town of Huatugou, Qinghai-Tibet Plateau, China. An analysis of this strain's phenotypic, chemotaxonomic, and genomic...
Strain Y74 was an isolate from the sandy soil in the town of Huatugou, Qinghai-Tibet Plateau, China. An analysis of this strain's phenotypic, chemotaxonomic, and genomic characteristics established the relationship of the isolate with the genus Planococcus. Strain Y74 was able to grow between 4 and 42°C (with an optimum temperature of 28°C) at pH values of 6-8.5 and in 0%-7% (w/v) NaCl. The dominant quinones were MK-8 and MK-7. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and an unknown phospholipid. The majority of the fatty acid content was anteiso-C (28.8%) followed by C ω7c alcohol (20.9%) and iso-C (13.4%). The 16S rRNA gene sequence similarity analysis demonstrated a stable branch formed by strain Y74 and Planococcus halotolerans SCU63 (99.66%). The digital DNA-DNA hybridization between these two strains was 57.2%. The G + C content in the DNA of Y74 was 44.5 mol%. In addition, the morphological, physiological, and chemotaxonomic pattern clearly differentiated the isolates from their known relatives. In conclusion, the strain Y74 (=JCM 32826 = CICC24461 ) represents a novel member of the genus Planococcus, for which the name Planococcus antioxidans sp. nov. is proposed. Strain Y74 was found to have potent antioxidant activity via its hydrogen peroxide tolerance and its 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging activity. The DPPH radical-scavenging activity was determined to be 40.2 ± 0.7%. The genomic analysis indicated that six peroxidases genes, one superoxide dismutase gene, and one dprA (DNA-protecting protein) are present in the genome of Y74 .
Topics: Antioxidants; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Genome, Bacterial; Planococcus Bacteria; Sequence Analysis, DNA; Soil Microbiology; Tibet; Whole Genome Sequencing
PubMed: 32162498
DOI: 10.1002/mbo3.1028 -
Scientific Reports Feb 2020Intestinal flora plays an important role in inflammatory response to systemic or local organs of its host. High calorie diet has been shown to aggravate the condition of...
Intestinal flora plays an important role in inflammatory response to systemic or local organs of its host. High calorie diet has been shown to aggravate the condition of pneumonia and delay recovery, especially in children. However, the underlying mechanisms remain unclear. This study placed SPF rats in a conventional environment, high calorie diet or LPS atomization was performed respectively or combined. Analysis of high-throughput sequencing of intestinal content combined with animal weight, organ index, serum inflammatory factors indicators and bioinformatics found that after pulmonary infection combined with a high-calorie diet, rats showed significant changes such as weight loss and increased lung weight index, and their lung and intestinal tissues showed more obvious inflammatory changes. And its gut flora structure suggests, the abundance of Leuconostocaceae in significantly reduced; abundance of Staphylococcus, Planococcaceae, Staphylococcus, Staphylococcaceae, Bacillales, Gemellales and Aerococcus significant increased. The study showed that high calorie diet and LPS atomization synergistically promoted pneumonia process in rat pups, which is related to changes in structure of intestinal flora. It is worth noting that pneumonia rats fed by convention diet also causing intestinal flora imbalance.
Topics: Animals; Animals, Newborn; Body Weight; Diet; Gastrointestinal Microbiome; High-Throughput Nucleotide Sequencing; Humans; Inflammation; Intestinal Mucosa; Lipopolysaccharides; Lung; Male; Pneumonia; Rats; Rats, Sprague-Dawley
PubMed: 32015367
DOI: 10.1038/s41598-020-58632-0 -
Frontiers in Microbiology 2019The family / is a taxonomically heterogeneous assemblage of >100 species classified within 13 genera, many of which are polyphyletic. Exhibiting considerable...
The family / is a taxonomically heterogeneous assemblage of >100 species classified within 13 genera, many of which are polyphyletic. Exhibiting considerable phylogenetic overlap with other families, primarily , the evolutionary history of this family, containing the potent mosquitocidal species , remains incoherent. To develop a reliable phylogenetic and taxonomic framework for the family / and its genera, we report comprehensive phylogenetic and comparative genomic analyses on 124 genome sequences from all available / and representative species. Phylogenetic trees were constructed based on multiple datasets of proteins including 819 core proteins for this group and 87 conserved proteins. Using the core proteins, pairwise average amino acid identity was also determined. In parallel, comparative analyses on protein sequences from these species have identified 92 unique molecular markers (synapomorphies) consisting of conserved signature indels that are specifically shared by either the entire family / or different monophyletic clades present within this family, enabling their reliable demarcation in molecular terms. Based on multiple lines of investigations, 18 monophyletic clades can be reliably distinguished within the family / based on their phylogenetic affinities and identified molecular signatures. Some of these clades are comprised of species from several polyphyletic genera within this family as well as other families. Based on our results, we are proposing the creation of three novel genera within the family /, namely gen. nov., gen. nov., and gen. nov., as well as the transfer of 25 misclassified species from the families / and into these three genera and in , , , and genera. These amendments establish a coherent taxonomy and evolutionary history for the family /, and the described molecular markers provide novel means for diagnostic, genetic, and biochemical studies. Lastly, we are also proposing a consolidation of the family within the emended family .
PubMed: 32010063
DOI: 10.3389/fmicb.2019.02821 -
Microbial Cell Factories Jan 2020The ureolytic bacterium Sporosarcina pasteurii is well-known for its capability of microbially induced calcite precipitation (MICP), representing a great potential in...
BACKGROUND
The ureolytic bacterium Sporosarcina pasteurii is well-known for its capability of microbially induced calcite precipitation (MICP), representing a great potential in constructional engineering and material applications. However, the molecular mechanism for its biomineralization remains unresolved, as few studies were carried out.
RESULTS
The addition of urea into the culture medium provided an alkaline environment that is suitable for S. pasteurii. As compared to S. pasteurii cultivated without urea, S. pasteurii grown with urea showed faster growth and urease production, better shape, more negative surface charge and higher biomineralization ability. To survive the unfavorable growth environment due to the absence of urea, S. pasteurii up-regulated the expression of genes involved in urease production, ATPase synthesis and flagella, possibly occupying resources that can be deployed for MICP. As compared to non-mineralizing bacteria, S. pasteurii exhibited more negative cell surface charge for binding calcium ions and more robust cell structure as nucleation sites. During MICP process, the genes for ATPase synthesis in S. pasteurii was up-regulated while genes for urease production were unchanged. Interestingly, genes involved in flagella were down-regulated during MICP, which might lead to poor mobility of S. pasteurii. Meanwhile, genes in fatty acid degradation pathway were inhibited to maintain the intact cell structure found in calcite precipitation. Both weak mobility and intact cell structure are advantageous for S. pasteurii to serve as nucleation sites during MICP.
CONCLUSIONS
Four factors are demonstrated to benefit the super performance of S. pasteurii in MICP. First, the good correlation of biomass growth and urease production of S. pasteurii provides sufficient biomass and urease simultaneously for improved biomineralization. Second, the highly negative cell surface charge of S. pasteurii is good for binding calcium ions. Third, the robust cell structure and fourth, the weak mobility, are key for S. pasteurii to be nucleation sites during MICP.
Topics: ATP Synthetase Complexes; Biomineralization; Calcium Carbonate; Culture Media; Gene Expression Profiling; Genome, Bacterial; Microscopy, Electron, Scanning; Sporosarcina; Urea; Urease
PubMed: 31973723
DOI: 10.1186/s12934-020-1281-z -
Microorganisms Dec 2019Antibiotic resistance is a global issue which is magnified by interspecies horizontal gene transfer. Understanding antibiotic resistance in bacteria in a natural setting...
Antibiotic resistance is a global issue which is magnified by interspecies horizontal gene transfer. Understanding antibiotic resistance in bacteria in a natural setting is crucial to check whether they are multidrug resistant (MDR) and possibly avoid outbreaks. In this study, we have isolated several antibiotic-resistant bacteria (ARB) ( = 128) from the mangroves in Kerala, India. ARBs were distributed based on antibiotics ( = 1.6 × 10). The 16S rRNA gene characterization revealed dominance by Bacillaceae (45%), Planococcaceae (22.5%), and Enterobacteriaceae (17.5%). A high proportion of the isolates were MDR (75%) with maximum resistance to methicillin (70%). Four isolates affiliated to plant-growth promoters, probiotics, food, and human pathogens were resistant to all antibiotics indicating the seriousness and prevalence of MDR. A significant correlation (R = 0.66; = 2.5 × 10) was observed between MDR and biofilm formation. Antagonist activity was observed in 62.5% isolates. Gram-positive isolates were more susceptible to antagonism (75.86%) than gram-negative (36.36%) isolates. Antagonism interactions against gram-negative isolates were lower (9.42%) when compared to gram-positive isolates (89.85%). Such strong antagonist activity can be harnessed for inspection of novel antimicrobial mechanisms and drugs. Our study shows that MDR with strong biofilm formation is prevalent in natural habitat and if acquired by deadly pathogens may create havoc in public health.
PubMed: 31835720
DOI: 10.3390/microorganisms7120678 -
Scientific Reports Oct 2019Bacteria swim and swarm by rotating the micrometers long, helical filaments of their flagella. They change direction by reversing their flagellar rotation, which...
Bacteria swim and swarm by rotating the micrometers long, helical filaments of their flagella. They change direction by reversing their flagellar rotation, which switches the handedness of the filament's supercoil. So far, all studied functional filaments are composed of a mixture of L- and R-state flagellin monomers. Here we show in a study of the wild type Firmicute Kurthia sp., that curved, functional filaments can adopt a conformation in vivo that is closely related to a uniform, all-L-state. This sheds additional light on transitions of the flagellar supercoil and uniquely reveals the atomic structure of a wild-type flagellar filament in vivo, including six residues showing clearly densities of O-linked glycosylation.
Topics: Anisotropy; Bacterial Proteins; Cryoelectron Microscopy; Firmicutes; Flagella; Flagellin; Fourier Analysis; Glycosylation; Planococcaceae; Software
PubMed: 31628388
DOI: 10.1038/s41598-019-51440-1 -
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