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.

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 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 Novel Diagnostic Algorithm for Identification of Mycobacteria Using Genus-Specific Amplification of the 16S-23S rRNA Gene Spacer and Restriction Endonucleases

2000 ◽  
Vol 38 (3) ◽  
pp. 1094-1104 ◽  
Author(s):  
Andreas Roth ◽  
Udo Reischl ◽  
Anna Streubel ◽  
Ludmila Naumann ◽  
Reiner M. Kroppenstedt ◽  
...  
Keyword(s):  
16S Rdna ◽  
Restriction Analysis ◽  
Diagnostic Algorithm ◽  
Species Level ◽  
23S Rrna ◽  
Rrna Gene ◽  
Correct Identification ◽  
Mycobacterium Fortuitum ◽  
Mycobacterium Chelonae ◽  
Rdna Sequencing

A novel genus-specific PCR for mycobacteria with simple identification to the species level by restriction fragment length polymorphism (RFLP) was established using the 16S-23S ribosomal RNA gene (rDNA) spacer as a target. Panspecificity of primers was demonstrated on the genus level by testing 811 bacterial strains (122 species in 37 genera from 286 reference strains and 525 clinical isolates). All mycobacterial isolates (678 strains among 48 defined species and 5 indeterminate taxons) were amplified by the new primers. Among nonmycobacterial isolates, only Gordonia terrae was amplified. The RFLP scheme devised involves estimation of variable PCR product sizes together with HaeIII and CfoI restriction analysis. It yielded 58 HaeIII patterns, of which 49 (84%) were unique on the species level. Hence,HaeIII digestion together with CfoI results was sufficient for correct identification of 39 of 54 mycobacterial taxons and one of three or four of seven RFLP genotypes found inMycobacterium intracellulare and Mycobacterium kansasii, respectively. Following a clearly laid out diagnostic algorithm, the remaining unidentified organisms fell into five clusters of closely related species (i.e., the Mycobacterium aviumcomplex or Mycobacterium chelonae-Mycobacterium abscessus) that were successfully separated using additional enzymes (TaqI, MspI, DdeI, orAvaII). Thus, next to slowly growing mycobacteria, all rapidly growing species studied, including M. abscessus,M. chelonae, Mycobacterium farcinogenes,Mycobacterium fortuitum, Mycobacterium peregrinum, and Mycobacterium senegalense (with a very high 16S rDNA sequence similarity) were correctly identified. A high intraspecies sequence stability and the good discriminative power of patterns indicate that this method is very suitable for rapid and cost-effective identification of a wide variety of mycobacterial species without the need for sequencing. Phylogenetically, spacer sequence data stand in good agreement with 16S rDNA sequencing results, as was shown by including strains with unsettled taxonomy. Since this approach recognized significant subspecific genotypes while identification of a broad spectrum of mycobacteria rested on identification of one specific RFLP pattern within a species, this method can be used by both reference (or research) and routine laboratories.

Surface microbial consortia from Livarot, a French smear-ripened cheese

2011 ◽  
Vol 57 (8) ◽  
pp. 651-660 ◽  
Author(s):  
Sandra Larpin-Laborde ◽  
Muhammad Imran ◽  
Catherine Bonaïti ◽  
Nagamani Bora ◽  
Roberto Gelsomino ◽  
...  
Keyword(s):  
Geotrichum Candidum ◽  
Microbial Consortia ◽  
Gram Negative Bacteria ◽  
Gram Positive ◽  
Gram Negative ◽  
Gram Positive Bacteria ◽  
Rdna Sequencing ◽  
Negative Role ◽  
Cleaning Procedures ◽  
High Level

The surface microflora (902 isolates) of Livarot cheeses from three dairies was investigated during ripening. Yeasts were mainly identified by Fourier transform infrared spectroscopy. Geotrichum candidum was the dominating yeast among 10 species. Bacteria were identified using Biotype 100 strips, dereplicated by repetitive extragenic palindromic PCR (rep-PCR); 156 representative strains were identified by either BOX-PCR or (GTG)5-PCR, and when appropriate by 16S rDNA sequencing and SDS–PAGE analysis. Gram-positive bacteria accounted for 65% of the isolates and were mainly assigned to the genera Arthrobacter , Brevibacterium , Corynebacterium , and Staphylococcus . New taxa related to the genera Agrococcus and Leucobacter were found. Yeast and Gram-positive bacteria strains deliberately added as smearing agents were sometimes undetected during ripening. Thirty-two percent of the isolates were Gram-negative bacteria, which showed a high level of diversity and mainly included members of the genera Alcaligenes , Hafnia , Proteus , Pseudomonas , and Psychrobacter . Whatever the milk used (pasteurized or unpasteurized), similar levels of biodiversity were observed in the three dairies, all of which had efficient cleaning procedures and good manufacturing practices. It appears that some of the Gram-negative bacteria identified should now be regarded as potentially useful in some cheese technologies. The assessment of their positive versus negative role should be objectively examined.

scholarly journals Isolation and Identification of Pesticides Degrading Bacteria from Farmland Soil

2019 ◽  
Vol 35 (2) ◽  
pp. 90-94
Author(s):  
Md Atikur Rahman ◽  
ASM Shamsul Arefin ◽  
Otun Saha ◽  
Md Mizanur Rahaman
Keyword(s):  
16S Rdna ◽  
Restriction Analysis ◽  
Bacterial Strains ◽  
Biochemical Tests ◽  
Isolation And Identification ◽  
Rdna Sequencing ◽  
Degrading Bacteria ◽  
Farmland Soil ◽  
Wide Range ◽  
Dna Restriction

Pesticides are recognized to be the threat to the environment and associated with a wide range of serious diseases including respiratory diseases, cancer and even birth defects. In this study, six-different bacterial strains capable of degrading Carbofuran, Emamectin Benzoate and Thiamethoxam were isolated from eight different soil samples. The isolates were characterized by using different conventional and molecular methods. The strains were identified molecularly into different genotypes using amplified ribosomal DNA restriction analysis (ARDRA) and partial sequencing of 16S rDNA. The ARDRA pattern clustered them into 3 groups. Among the isolates three were identified as Achromobacter spp. and one as Diaphorobacter sp. by biochemical tests. It was further confirmed by the partial 16S rDNA sequencing. The two identified potential bacteria can be used for biodegradation of different pesticides which can have a significant environmental impact in soil farm. Bangladesh J Microbiol, Volume 35 Number 2 December 2018, pp 90-94

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.

scholarly journals Actinomycetes isolated from soils collected in adjacent areas of Hochiminh city: sources of potential antibiotics

2015 ◽  
Vol 18 (2) ◽  
pp. 75-84
Author(s):  
Huyen Thi Pham ◽  
Thu Huynh ◽  
Phuong Ngoc Uyen Pham ◽  
Tao Thi Ly Vo
Keyword(s):  
Staphylococcus Aureus ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Soil Samples ◽  
Viet Nam ◽  
Gram Negative Bacteria ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Sequencing Method ◽  
Rdna Sequencing ◽  
Resistant Form

Actinomycetes are Gram-positive bacteria resembling filamentous fungi in shape. The majority of natural antibiotics useful today are obtained from actinomycetes. This study isolated actinomycetes from soil samples collected in adjacent areas of HoChiMinh City, Việt Nam. One of the isolates was Streptomyces flaveus determined using 16S rDNA sequencing method. S. flaveus was capable of inhibiting the growth of both Gram-positive and Gram-negative bacteria, especially the Staphylococcus aureus and its multiantibiotic resistant form – the methicillin resistant Staphylococcus aureus (MRSA). MRSA is at present a serious threat to human health not only in Vietnam but also in many other countries around the world. However, antibiotics indicated for the treatment of diseases caused by the MRSA are currently not much effective. Thus, S. flaveus in this study will be a source of potential antibiotics against diseases caused by the MRSA.

scholarly journals Rhizosphere Bacterial Population Flux in Golf Course Putting Greens in the Southeastern United States

HortScience ◽  
2004 ◽  
Vol 39 (7) ◽  
pp. 1754-1758 ◽  
Author(s):  
M.L. Elliott ◽  
E.A. Guertal ◽  
H.D. Skipper
Keyword(s):  
North Carolina ◽  
South Carolina ◽  
Cynodon Dactylon ◽  
Creeping Bentgrass ◽  
Fluorescent Pseudomonads ◽  
Culturable Bacteria ◽  
Gram Positive ◽  
Putting Greens ◽  
Gram Positive Bacteria ◽  
Heat Tolerant

The rhizospheres of creeping bentgrass (Agrostis palustris Huds.) and hybrid bermudagrass (Cynodon dactylon (L.) Pers. × C. transvaalensis Burtt-Davy) putting greens were sampled quarterly for 4 years. Six bacterial groups, including total aerobic bacteria, fluorescent pseudomonads, actinomycetes, Gram-negative bacteria, Gram-positive bacteria, and heat-tolerant bacteria, were enumerated. The putting greens were located in four geographic locations (bentgrass in Alabama and North Carolina; bermudagrass in Florida and South Carolina) and were maintained according to local maintenance practices. Significant effects were observed for sampling date, turfgrass species and location, with most variation due to either turfgrass species or location. Bentgrass roots had significantly greater numbers of fluorescent pseudomonads than bermudagrass roots, while bermudagrass roots had significantly greater numbers of Gram-positive bacteria, actinomycetes and heat-tolerant bacteria. The North Carolina or South Carolina locations always had the greatest number of bacteria in each bacterial group. For most sampling dates in all four locations and both turfgrass species, there was a minimum, per gram dry root, of 107 CFUs enumerated on the total aerobic bacterial medium and a minimum of 105 CFUs enumerated on the actinomycete bacterial medium. Thus, it appears that in the southeastern U.S. there are large numbers of culturable bacteria in putting green rhizospheres that are relatively stable over time and geographic location.

Culture-independent phylogenetic analysis of the faecal flora of the rat

2003 ◽  
Vol 49 (10) ◽  
pp. 589-601 ◽  
Author(s):  
S P.J Brooks ◽  
M McAllister ◽  
M Sandoz ◽  
M L Kalmokoff
Keyword(s):  
16S Rdna ◽  
Comparative Sequence Analysis ◽  
Gram Positive ◽  
Faecal Flora ◽  
Comparative Sequence ◽  
Gram Positive Bacteria ◽  
Operational Taxonomic Units ◽  
Rdna Sequences ◽  
Culture Independent ◽  
Cultured Bacteria

The dominant faecal flora of the rat was determined using randomly cloned 16S rDNA comparative sequence analysis. A total of 109 near full-length 16S rDNA clones were sequenced, representing 69 unique 16S rRNA phylotypes or operational taxonomic units (OTUs). Estimates of species richness indicated that approximately 338 species were present in the faeces, suggesting that only 20% of species were identified. Only two of 39 Gram-negative clones aligned with previously cultured species, the remainder fell into a separate lineage within the Bacteroides–Cytophaga phylum. Several clones within this new group were related to 16S rDNA sequences previously identified from mouse faeces. Lactobacilli were the most abundant Gram-positive species, representing 23% of the total clones but only 7% of OTUs. The remaining Gram-positive clones were distributed among the Clostridium coccoides group (9%), the Clostridium leptum subgroup (18%), and throughout the low GC Gram-positive bacteria (13%). The majority of OTUs (63/69 or 91%) were less than 97% homologous to previously cultured bacteria. Faecal samples were also cultured using a variety of anaerobic media. With the exception of the lactobacilli, the cultured isolates demonstrated low species diversity and poorly reflected the population, as defined through comparative sequence analysis.Key words: rat, faeces, 16S rDNA, phylogenetic, cultured bacteria.

The microbial community analysis of a 5-stage BNR process with step feed system

2003 ◽  
Vol 48 (8) ◽  
pp. 135-141 ◽  
Author(s):  
H.W. Lee ◽  
S.Y. Lee ◽  
J.O. Lee ◽  
H.G. Kim ◽  
J.B. Park ◽  
...  
Keyword(s):  
16S Rdna ◽  
Community Analysis ◽  
Cell Number ◽  
Total Cell ◽  
Microbial Community Analysis ◽  
Feed System ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Cell Counts

The microbial communities of 5-stage BNR activated sludge samples were analyzed using fluorescence in-situ hybridization (FISH) and 16S rDNA characterization. The total cell numbers of each reactor were from 2.36 × 109 cells/ml to 2.83 × 109 cells/ml. From 56.5% to 62.0% of total DAPI cell counts were hybridized to the most bacterial specific probe EUB 338. Among them, b-proteobacteria were most dominant in each tank. The number of phosphate accumulating organisms (PAOs) was almost 50% of the total cell number in anoxic-1 tank, and these results indicate that this process has a high content of denitrifying phosphorus accumulating organisms (dPAOs). In contrast with FISH, 16S rDNA analysis showed that dominant groups were the Cytophaga-Flavobacterium group and high G+C% gram-positive bacteria, which were determined as PAOs in anoxic-1 tank. The beta subclass Proteobacteria did not accumulate a large amount of polyphosphate. The overall results indicate that high G+C% gram-positive bacteria and the Cytophaga-Flavobacterium group might play a key role as dPAOs in this process.

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