Phylogenetic analysis of bacterial populations in waters of the former Texcoco Lake, Mexico

2004 ◽  
Vol 50 (12) ◽  
pp. 1049-1059 ◽  
Author(s):  
Janet Jan-Roblero ◽  
Xochitl Magos ◽  
Luis Fernández ◽  
César Hernández-Rodríguez ◽  
Sylvie Le Borgne
Keyword(s):  
16S Rdna ◽  
Bacterial Communities ◽  
Soda Lakes ◽  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Intergenic Spacer ◽  
Molecular Techniques ◽  
Preliminary Evaluation ◽  
Gram Positive ◽  
Gram Positive Bacteria

Molecular techniques were used to compare the compositions of the bacterial communities of the 2 following lagoons from the former soda Texcoco Lake, Mexico: the restored Facultativa lagoon and the Nabor Carrillo lagoon. Ribosomal intergenic spacer analysis (RISA) revealed that bacterial communities of the 2 lagoons were different and presented a relatively low diversity. Clone libraries of 16S rDNA genes were constructed, and significant phylotypes were distinguished by restriction fragment length polymorphism (RFLP). A representative clone from each phylotype was partially sequenced. Molecular identification and phylogenetic analyses based on ribosomal sequences revealed that the Facultativa lagoon harbored mainly γ- and β-Proteobacteria, low G+C Gram-positive bacteria, and several members of the Halobacteriaceae family of archaea. The Nabor Carrillo lagoon mainly included typical halophilic and alkaliphilic low G+C Gram-positive bacteria, γ-Proteobacteria, and β-Proteobacteria similar to those found in other soda lakes. Several probably noncultured new bacterial species were detected. Three strains were isolated from the Nabor Carrillo lagoon, their partial 16S rDNA sequences were obtained. On this basis, they were identified as Halomonas magadiensis (H1), Halomonas eurihalina (H2), and Staphylococcus sciuri (H3). This is the first study that uses molecular techniques to investigate potential genetic diversity in the Texcoco lakes. In this preliminary evaluation, we infer the presence of alkalophilic, halophilic, or haloalkaliphilic bacteria potentially useful for biotechnology.Key words: bacterial diversity, 16S rDNA gene, soda lakes, former soda Texcoco Lake, Mexico, alkaliphiles, halophiles, haloalkaliphiles.

Bacterial diversity associated with subalpine fir (Abies lasiocarpa) ectomycorrhizae following wildfire and salvage-logging in central British Columbia

2002 ◽  
Vol 48 (7) ◽  
pp. 611-625 ◽  
Author(s):  
Madhukar B Khetmalas ◽  
Keith N Egger ◽  
Hugues B Massicotte ◽  
Linda E Tackaberry ◽  
M Jill Clapperton
Keyword(s):  
Bacterial Diversity ◽  
16S Rdna ◽  
Bacterial Communities ◽  
Restriction Analysis ◽  
Rrna Gene ◽  
Abies Lasiocarpa ◽  
Gram Positive ◽  
Salvage Logging ◽  
Gram Positive Bacteria ◽  
Significant Difference

To assess the effect of fire and salvage logging on the diversity of mycorrhizal–bacterial communities, bacteria associated with Cenococcum, Thelephora, Tomentella, Russulaceae, and E-strain ectomycorrhizae (ECM) of Abies lasiocarpa seedlings were characterized using two approaches. First, bacteria were isolated and characterized by Biolog©, gas chromatography fatty acid methyl ester (GC-FAME), and amplified 16S rDNA restriction analysis (ARDRA). The bacterial communities retrieved from ECM from both sites were dominated by Proteobacteria (groups gamma and beta). Pseudomonas was the most common genus isolated, followed by Variovorax, Burkholderia, and Xanthomonas. Gram-positive isolates (mostly high-G+C Gram-positive bacteria) were more frequently retrieved on the burned-salvaged site, many commonly associated with the two ascomycete ECM, Cenococcum and E-strain. Pseudomonas species were retrieved more frequently from Thelephora. Although actinomycetes were isolated from all sites, almost no actinomycetes or other Gram-positive bacteria were isolated from either Thelephora or Tomentella. Second, amplified 16S rRNA gene sequences were amplified directly from root tips and then cloned into the plasmid vector pAMP1, followed by restriction analysis. This technique distinguished more genotypes than isolates retrieved by culturing methods, but generally, results were similar in that the largest proportion of the bacteria were putatively Gram-negative; putative Gram-positive bacteria were fewer and most were from the burned–salvaged site. Direct cloning resulted in many patterns that did not match any identified isolates, suggesting that a large proportion of clones were unique or not culturable by the methods used. Analysis for both protocols showed no significant difference in bacterial diversity between the burned–salvaged and unburned sites. Key words: rhizosphere bacteria, ARDRA, 16S rDNA, Biolog©, GC-FAME.

scholarly journals Preliminary Evaluation of the Research-Use-Only (RUO) iCubate iC-GPC Assay for Identification of Select Gram-Positive Bacteria and Their Resistance Determinants in Blood Culture Broths: TABLE 1

2015 ◽  
Vol 53 (12) ◽  
pp. 3931-3934 ◽  
Author(s):  
Blake W. Buchan ◽  
Garrett C. Reymann ◽  
Paul A. Granato ◽  
Brenda R. Alkins ◽  
Patricia Jim ◽  
...  
Keyword(s):  
Blood Culture ◽  
Staphylococcus Epidermidis ◽  
Bacterial Species ◽  
Genetic Resistance ◽  
Preliminary Evaluation ◽  
Gram Positive ◽  
Content Type ◽  
Gram Positive Bacteria ◽  
Resistance Determinants ◽  
On Demand

The iC-GPC assay (iCubate, Huntsville, AL) provides a molecular option for the rapid, on-demand analysis of positive blood cultures. A preliminary evaluation of the iC-GPC assay using 203 clinical or seeded specimens demonstrated a sensitivity of 93.8% to 100% and a specificity of 98.0% to 100% for the identification of five Gram-positive bacterial species (Staphylococcus aureus,Staphylococcus epidermidis,Streptococcus pneumoniae,Enterococcus faecalis, andEnterococcus faecium) and three associated genetic resistance determinants (mecA,vanA, andvanB) in positive blood culture broths.

scholarly journals Motility and adhesion through type IV pili in Gram-positive bacteria

2016 ◽  
Vol 44 (6) ◽  
pp. 1659-1666 ◽  
Author(s):  
Kurt H. Piepenbrink ◽  
Eric J. Sundberg
Keyword(s):  
Bacterial Species ◽  
Cellular Adhesion ◽  
Type Iv Pili ◽  
Twitching Motility ◽  
Gram Positive ◽  
Bacterial Surface ◽  
Gram Positive Bacteria ◽  
Type Iv ◽  
Current State ◽  
Highly Hydrophobic

Type IV pili are hair-like bacterial surface appendages that play a role in diverse processes such as cellular adhesion, colonization, twitching motility, biofilm formation, and horizontal gene transfer. These extracellular fibers are composed exclusively or primarily of many copies of one or more pilin proteins, tightly packed in a helix so that the highly hydrophobic amino-terminus of the pilin is buried in the pilus core. Type IV pili have been characterized extensively in Gram-negative bacteria, and recent advances in high-throughput genomic sequencing have revealed that they are also widespread in Gram-positive bacteria. Here, we review the current state of knowledge of type IV pilus systems in Gram-positive bacterial species and discuss them in the broader context of eubacterial type IV pili.

scholarly journals Relationships between Microbial Community Structure and Hydrochemistry in a Landfill Leachate-Polluted Aquifer

2001 ◽  
Vol 67 (10) ◽  
pp. 4619-4629 ◽  
Author(s):  
Wilfred F. M. Röling ◽  
Boris M. van Breukelen ◽  
Martin Braster ◽  
Bin Lin ◽  
Henk W. van Verseveld
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
16S Rdna ◽  
Microbial Community Structure ◽  
Landfill Leachate ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Numerical Comparison ◽  
Gram Positive ◽  
Gram Positive Bacteria

ABSTRACT Knowledge about the relationship between microbial community structure and hydrogeochemistry (e.g., pollution, redox and degradation processes) in landfill leachate-polluted aquifers is required to develop tools for predicting and monitoring natural attenuation. In this study analyses of pollutant and redox chemistry were conducted in parallel with culture-independent profiling of microbial communities present in a well-defined aquifer (Banisveld, The Netherlands). Degradation of organic contaminants occurred under iron-reducing conditions in the plume of pollution, while upstream of the landfill and above the plume denitrification was the dominant redox process. Beneath the plume iron reduction occurred. Numerical comparison of 16S ribosomal DNA (rDNA)-based denaturing gradient gel electrophoresis (DGGE) profiles of Bacteria andArchaea in 29 groundwater samples revealed a clear difference between the microbial community structures inside and outside the contaminant plume. A similar relationship was not evident in sediment samples. DGGE data were supported by sequencing cloned 16S rDNA. Upstream of the landfill members of the β subclass of the class Proteobacteria(β-proteobacteria) dominated. This group was not encountered beneath the landfill, where gram-positive bacteria dominated. Further downstream the contribution of gram-positive bacteria to the clone library decreased, while the contribution of δ-proteobacteria strongly increased and β-proteobacteria reappeared. The β-proteobacteria (Acidovorax,Rhodoferax) differed considerably from those found upstream (Gallionella, Azoarcus). Direct comparisons of cloned 16S rDNA with bands in DGGE profiles revealed that the data from each analysis were comparable. A relationship was observed between the dominant redox processes and the bacteria identified. In the iron-reducing plume members of the familyGeobacteraceae made a strong contribution to the microbial communities. Because the only known aromatic hydrocarbon-degrading, iron-reducing bacteria areGeobacter spp., their occurrence in landfill leachate-contaminated aquifers deserves more detailed consideration.

scholarly journals Second Harmonic Generation Spectroscopy of Membrane Probe Dynamics in Gram-Positive Bacteria

2019 ◽  
Author(s):  
L. N. Miller ◽  
W. T. Brewer ◽  
J. D. Williams ◽  
E. M. Fozo ◽  
T. R. Calhoun
Keyword(s):  
Second Harmonic Generation ◽  
Small Molecules ◽  
Harmonic Generation ◽  
Second Harmonic ◽  
Bacterial Species ◽  
Gram Positive ◽  
Flip Flop ◽  
Bacterial Membranes ◽  
Gram Positive Bacteria ◽  
Fluorescence Measurements

ABSTRACTBacterial membranes are complex mixtures with dispersity that is dynamic over scales of both space and time. In order to capture adsorption onto and transport within these mixtures, we conduct simultaneous second harmonic generation (SHG) and two photon fluorescence measurements on two different gram-positive bacterial species as the cells uptake membrane-specific probe molecules. Our results show that SHG can not only monitor the movement of small molecules across membrane leaflets, but is also sensitive to higher-level ordering of the molecules within the membrane. Further, we show that the membranes of Staphylococcus aureus remain more dynamic after longer times at room temperature in comparison to Enterococcus faecalis. Our findings provide insight into the variability of activities seen between structurally similar molecules in gram-positive bacteria while also demonstrating the power of SHG to examine these dynamics.STATEMENT OF SIGNIFICANCEBacterial membranes are highly adept at discerning and modifying their interactions with different small molecules in their environment. Here we show how second harmonic generation (SHG) spectroscopy can track the dynamics of structurally similar membrane probes in two gram-positive bacterial species. Our results reveal behavior that is dependent on both the probe molecule and the membrane composition. Specifically, we observe flip-flop between leaflets for one molecule, while the other molecule produces a signal indicative of larger scale ordering in the membrane. These phenomena can all be explained by considering potential differences in the membrane fluidity and surface charge between the two bacterial species. Overall, our work highlights the dynamic differences between bacterial membranes and SHG’s sensitivity to probing these systems.

scholarly journals Molecular Characterization of Zinc (Zn) Resistant Bacteria in Banger River, Pekalongan, Indonesia

2018 ◽  
Vol 10 (3) ◽  
pp. 622-628
Author(s):  
Fitri Arum Sasi ◽  
Hermin Pancasakti Kusumaningrum ◽  
Anto Budiharjo
Keyword(s):  
Bacterial Species ◽  
Selective Medium ◽  
Resistant Bacteria ◽  
Gram Negative Bacteria ◽  
Gram Positive ◽  
Gram Negative ◽  
Indigenous Bacteria ◽  
Gram Positive Bacteria ◽  
Sequences Analysis

Indigenous bacteria are able to remove the metals contamination in environment. This study aimed to assess the resistance of bacterial species to Zinc (Zn) in Banger River, Pekalongan City. The bacteria from three different parts of Banger River were isolated and inoculated in Zn-selective medium. Then, molecular identification to determine the bacteria species was conducted using polymerase chain reaction (PCR) by applying forward-reverse 16SrRNA gene primers. The sequences analysis was conducted using MUSCLE and MEGA6. There were seven dominant species that possibly resistant to Zn. Approximately, every isolate could reach more than 95 % from 2000 ppm of Zn in the medium. The higher absorption of Zn was found in Z5 isolate. The seven bacteria species were clustered into nine genera i.e. Klebsiela, Xenorhabdus, Cronobacter, Enterobacter, Escherichia, Shigella and Sporomusa known as Gram Negative bacteria and Clostridium and Bacillus as Gram Positive bacteria. In Gram Positive bacteria, especially Bacillus sp, carboxyl group in peptidoglycan play a role as metal binder. In Gram-negative bacteria, lipopolysaccharide (LPS) which is highly anionic component on the outer membrane, able to catch the Zn. Besides that, Enterobacter activates endogen antioxidants such as glutathione peroxidase (GSHPx), glutathione reductase (GR), catalase (CAT) and superoxide dismutase (SOD). The research found there was possible seven novel indigenous bacteria species in Banger that able to remove Zn from the sediment extremely. This finding can be developed as an eco-friendly approach to reduce metals pollution using local microorganisms.

Development of the iCubate Molecular Diagnostic Platform Utilizing Amplicon Rescue Multiplex Polymerase Chain Reaction

2019 ◽  
Vol 15 (7) ◽  
pp. 1598-1608
Author(s):  
Hongna Liu ◽  
Kathryn Heflin ◽  
Jian Han ◽  
Matt Conover ◽  
Leslie Wagner ◽  
...  
Keyword(s):  
Limit Of Detection ◽  
Bacterial Species ◽  
Bloodstream Infections ◽  
Cross Reactivity ◽  
Blood Cultures ◽  
Molecular Diagnostic ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
High Level

We utilized Amplicon-Rescue Multiplex PCR (ARM-PCR) and microarray hybridization to develop and validate the iC-GPC Assay, a multiplexed, in vitro diagnostic test that identifies five of the most common gram positive bacteria and three clinically relevant resistance markers associated with bloodstream infections (BSI). The iC-GPC Assay is designed for use with the iC-System™, which automates sample preparation, ARM-PCR, and microarray detection within a closed cassette. Herein, we determined the limit of detection for each of the iC-GPC Assay targets to be between 3.0 × 105–1.7 × 107 CFU/mL, well below clinically relevant bacterial levels for positive blood cultures. Additionally, we tested 106 strains for assay inclusivity and observed a target performance of 99.4%. 95 of 96 non-target organisms tested negative for cross-reactivity, thereby assuring a high level of assay specificity. Overall performance above 99% was observed for iC-GPC Assay reproducibility studies across multiple sites, operators and cassette lots. In conclusion, the iC-GPC Assay is capable of accurately and rapidly identifying bacterial species and resistance determinants present in blood cultures containing gram positive bacteria. Utilizing molecular diagnostics like the iC-GPC Assay will decrease time to treatment, healthcare costs, and BSI-related mortality.

scholarly journals Polymorphism of the Polyketide Synthase Gene phlD in Biocontrol Fluorescent Pseudomonads Producing 2,4-Diacetylphloroglucinol and Comparison of PhlD with Plant Polyketide Synthases

2001 ◽  
Vol 14 (5) ◽  
pp. 639-652 ◽  
Author(s):  
Alban Ramette ◽  
Yvan Moënne-Loccoz ◽  
Geneviève Défago
Keyword(s):  
16S Rdna ◽  
Polyketide Synthase ◽  
Restriction Analysis ◽  
Polyketide Synthases ◽  
Fluorescent Pseudomonads ◽  
Phylogenetic Groups ◽  
Gram Positive ◽  
Restriction Patterns ◽  
Gram Positive Bacteria ◽  
Rdna Sequencing

Many biocontrol fluorescent pseudomonads can protect plants from soilborne fungal pathogens through production of the antifungal secondary metabolite 2,4-diacetylphloroglucinol (Phl). One of the phl biosynthetic genes, phlD, encodes a polyketide synthase similar to plant chalcone synthases. Here, restriction analysis of phlD from 39 Phl+ biocontrol fluorescent pseudomonads yielded seven different banding patterns. The gene was sequenced in seven strains, representing the different restriction patterns. Cluster analysis of phlD restriction data or phlD sequences indicated that phlD polymorphism was high, and two main clusters were obtained when predicted PhlD sequences were compared. When the seven PhlD sequences were studied with those of other procaryotic polyketide synthases (gram-positive bacteria) and plant chalcone synthases, however, Phl+ pseudomonads, gram-positive bacteria, and plants clustered separately. Yet, sequence analysis of active site regions for PhlD and plant chalcone synthases revealed that PhlD can be considered a member of the chalcone synthase family, which may be interpreted as convergent evolution of key enzymes involved in secondary metabolism. For the 39 Phl+ pseudomonads, a relationship was found among phlD restriction patterns, phylogenetic groups defined by 16S rDNA restriction analysis (confirmed by 16S rDNA sequencing), and production levels of Phl in vitro.

Characterization of halophilic bacteria from environmental samples from the brackish water of Pulicat Lake, India

Biologia ◽  
2011 ◽  
Vol 66 (5) ◽  
Author(s):  
Harmesh Sahay ◽  
Surendra Singh ◽  
Rajeev Kaushik ◽  
Anil Saxena ◽  
Dilip Arora
Keyword(s):  
16S Rdna ◽  
Brackish Water ◽  
Phylogenetic Analyses ◽  
Halophilic Bacteria ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Gram Positive Bacteria ◽  
Nutrient Agar Medium

AbstractCulture dependent phenotypic characterization and 16S rDNA based phylogenetic analyses were applied to study the aerobic halophilic bacterial population present in the Pulicat brackish-water Lake of India. Five different media were employed for isolation of bacteria. A total of 198 morphotypes were recovered, purified and screened for salt tolerance in nutrient agar medium amended with 5–25% NaCl. Based on 16S rDNA restriction fragment length polymorphism analysis with three restriction endonucleases, 51 isolates tolerant to 5% or more NaCl were grouped into 29 clusters. Phylogenetic analysis using 16S rRNA gene sequences revealed that 29 strains could further be allocated into two clades: 19 to Firmicutes and 10 to γ-Proteobacteria. Firmicutes included low G+C Gram-positive bacteria related to family Bacillaceae, which included five genera Bacillus, Virgibacillus, Rummelibacillus, Alkalibacillus and Halobacillus. Another genera included in Firmicutes was Salimicrobium halophilum. In the γ-Proteobacteria group, all the isolates belonged to one genus Halomonas, represented by six different species Halomonas salina, H. shengliensis, H. salifodinae, H. pacifica, H. aquamarina and H. halophila. Most of the isolates exhibited cellulase, xylanase, amylase and protease activities.

scholarly journals Molecular detection of Bartonella species and haemoplasmas in wild African buffalo (Syncerus caffer) in Mozambique, Africa

2018 ◽  
Vol 4 ◽  
Author(s):  
Luiz Ricardo Gonçalves ◽  
Marta Maria Geraldes Teixeira ◽  
Adriana Carlos Rodrigues ◽  
Natalia Serra Mendes ◽  
Carlos Antonio Matos ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Animal Health ◽  
Species Conservation ◽  
Release Site ◽  
Molecular Techniques ◽  
African Buffalo ◽  
Syncerus Caffer ◽  
Mammal Species ◽  
The Impact

AbstractThe African buffalo (Syncerus caffer), a mammal species whose population is declining, can play a role as a reservoir or carrier of a wide number of arthropod-borne pathogens. Translocation procedures have been used as an alternative approach for species conservation. However, the veterinary aspects of this sort of procedures are extremely important to minimize the impact on animal health. In order to detectBartonellaand haemoplasmas, two important group of bacterial that have an impact in both human and animal health, EDTA whole-blood samples were screened for the presence of these bacterial pathogens by molecular techniques. As a result, a molecular occurrence of 4.1 and 15.4% forBartonellaspp. and haemoplasmas, respectively, was reported among 97 wild buffaloes sampled during a translocation procedure from Marromeu to Gorongosa Reserve, Mozambique. Additionally, phylogenetic analyses of the obtained sequences were conducted. At least, three bovine-associated pathogens, namelyB. bovis,M. wenyoniiand ‘CandidatusM. haemobos’, as well as a probably newBartonellagenotype/species were detected inS. caffer.Further studies are needed in order to determine whether these bacterial species may cause impact in buffaloes and other sympatric ruminant species living in the release site.

Sign in / Sign up

Export Citation Format

Share Document