Amplified rDNA Restriction Analysis (ARDRA) for monitoring of potentially toxic cyanobacteria in water samples

2008 ◽  
Vol 56 (1) ◽  
pp. 75-82 ◽  
Author(s):  
Estelle Masseret ◽  
Assaf Sukenik
Keyword(s):  
Water Samples ◽  
Restriction Analysis ◽  
Toxic Cyanobacteria ◽  
Amplified Rdna Restriction Analysis

scholarly journals POTENTIAL TOXIC CYANOBACTERIA IN THREE LAKES OF JAKARTA-BOGOR AREA, INDONESIA

2008 ◽  
Vol 33 (1) ◽  
pp. 95-100
Author(s):  
Nining Betawati Prihantini ◽  
Arya Widyawan ◽  
Ronny Rianto ◽  
Yuni Ariyani ◽  
Wishnu Wardhana ◽  
...  
Keyword(s):  
Water Samples ◽  
Potential Toxicity ◽  
Planktothrix Agardhii ◽  
Toxic Cyanobacteria

The research was aimed to understand the composition and dominancy of aquatic microalgae, and to know the potential toxicity of Cyanobacteria occuring in three lakes of Jakarta-Bogor area. The study was done in 2006. The sampling sites were Lake Sunter 2 (North Jakarta), Lake Babakan (South Jakarta), and Lake Lido (Bogor). The water samples were taken using plankton-net (20 tan mesh) with horizontal tow. The results showed that. the number of microalgal genera in Sunter 2, Babakan, and Lido were different, i.e. 10 genera, 40 genera, and 14 genera, respectively. Cyanobacteria were dominant in Sunter 2 (96%) and Babakan (90.01%). The dominant Cyanobacteria in Sunter 2 was Planktothrix agardhii (53.48%), whereas in Babakan was Chroococcus dispersus (68.52%). The second abundant Cyanobacteria in Sunter 2 was Arthrospira (42.54%). Planktothrix agardhii and Arthrospira are known to produce harmful toxin.

scholarly journals Changes in Populations of Rhizosphere Bacteria Associated with Take-All Disease of Wheat

2001 ◽  
Vol 67 (10) ◽  
pp. 4414-4425 ◽  
Author(s):  
Brian B. McSpadden Gardener ◽  
David M. Weller
Keyword(s):  
Restriction Analysis ◽  
Selective Medium ◽  
Small Subset ◽  
Fluorescence Signal ◽  
Bacterial Populations ◽  
16S Sequencing ◽  
Knowing That ◽  
Amplified Rdna Restriction Analysis ◽  
Take All

ABSTRACT Take-all, caused by Gaeumannomyces graminis var. tritici, is one of the most important fungal diseases of wheat worldwide. Knowing that microbe-based suppression of the disease occurs in monoculture wheat fields following severe outbreaks of take-all, we analyzed the changes in rhizosphere bacterial communities following infection by the take-all pathogen. Several bacterial populations were more abundant on diseased plants than on healthy plants, as indicated by higher counts on a Pseudomonas-selective medium and a higher fluorescence signal in terminal restriction fragment length polymorphism analyses of amplified 16S ribosomal DNA (rDNA). Amplified rDNA restriction analysis (ARDRA) of the most abundant cultured populations showed a shift in dominance from Pseudomonasto Chryseobacterium species in the rhizosphere of diseased plants. Fluorescence-tagged ARDRA of uncultured rhizosphere washes revealed an increase in ribotypes corresponding to several bacterial genera, including those subsequently identified by partial 16S sequencing as belonging to species of alpha-, beta-, and gamma-proteobacteria, sphingobacteria, and flavobacteria. The functional significance of some of these populations was investigated in vitro. Of those isolated, only a small subset of the most abundantPseudomonas spp. and aphlD + Pseudomonas sp. showed any significant ability to inhibit G. graminis var. tritici directly. When cultured strains were mixed with the inhibitoryphlD + Pseudomonasstrain, the Chryseobacterium isolates showed the least capacity to inhibit this antagonist of the pathogen, indicating that increases in Chryseobacterium populations may facilitate the suppression of take-all by 2,4-diacetylphloroglucinol-producingphlD + pseudomonads.

scholarly journals Evaluating amplified rDNA restriction analysis assay for identification of bacterial communities

2009 ◽  
Vol 96 (4) ◽  
pp. 659-664 ◽  
Author(s):  
Menachem Y. Sklarz ◽  
Roey Angel ◽  
Osnat Gillor ◽  
M. Ines M. Soares
Keyword(s):  
Bacterial Communities ◽  
Restriction Analysis ◽  
Amplified Rdna Restriction Analysis

scholarly journals Amycolatopsis regifaucium sp. nov., a novel actinomycete that produces kigamicins

2007 ◽  
Vol 57 (11) ◽  
pp. 2562-2567 ◽  
Author(s):  
Geok Yuan Annie Tan ◽  
Stuart Robinson ◽  
Ernest Lacey ◽  
Roselyn Brown ◽  
Wonyong Kim ◽  
...  
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Restriction Analysis ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Closely Related Species ◽  
Phenotypic Profile ◽  
Soil Actinomycetes ◽  
Type Strains ◽  
Amplified Rdna Restriction Analysis

The taxonomic position of seven soil actinomycetes provisionally assigned to the genus Amycolatopsis was established in a polyphasic study. The isolates, which had identical 16S rRNA gene sequences, had closest similarity to the type strain of Amycolatopsis orientalis. A representative isolate, strain GY080T, had chemotaxonomic properties that were typical of the genus Amycolatopsis and could be distinguished from the type strain of A. orientalis using DNA–DNA relatedness data. All of the isolates shared a phenotypic profile that distinguished them from representatives of phylogenetically closely related species. Amplified rDNA restriction analysis showed that the isolates formed a homogeneous group that was distinctly separate from single-membered groups consisting of representative Amycolatopsis type strains, including that of A. orientalis. Based on the combined genotypic and phenotypic evidence, it is proposed that the seven isolates be classified as representatives of a novel species for which the name Amycolatopsis regifaucium sp. nov. is proposed. The type strain is GY080T (=DSM 45072T =NCIMB 14277T).

scholarly journals Frequency and Biodiversity of 2,4-Diacetylphloroglucinol-Producing Bacteria Isolated from the Maize Rhizosphere at Different Stages of Plant Growth

2000 ◽  
Vol 66 (3) ◽  
pp. 948-955 ◽  
Author(s):  
C. Picard ◽  
F. Di Cello ◽  
M. Ventura ◽  
R. Fani ◽  
A. Guckert
Keyword(s):  
Genetic Diversity ◽  
Plant Growth ◽  
Restriction Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Screening Programs ◽  
Maize Rhizosphere ◽  
High Level ◽  
Ribosomal Dnas ◽  
Amplified Rdna Restriction Analysis ◽  
Group 1

ABSTRACT A Pseudomonas 2,4-diacetylphloroglucinol (DAPG)-producing population that occurred naturally on the roots, in rhizosphere soil of Zea mays and in the nonrhizosphere soil was investigated in order to assess the microbial diversity at five stages of plant growth. A total of 1,716 isolates were obtained, and 188 of these isolates were able to produce DAPG. DAPG producers were isolated at each stage of plant growth, indicating that the maize rhizosphere is colonized by natural DAPG producers throughout development. The frequency of DAPG producers was very low in the first stage of plant growth and increased over time. An analysis of the level of biodiversity of the DAPG producers at the species level was performed by comparing the AluI restriction patterns of the 16S ribosomal DNAs (rDNAs) amplified by PCR from 167 isolates. This comparison allowed us to cluster the isolates into four amplified rDNA restriction analysis (ARDRA) groups, and the main group (ARDRA group 1) contained 89.8% of the isolates. The diversity of the 150 isolates belonging to ARDRA group 1 was analyzed by the random amplified polymorphic DNA (RAPD) technique. An analysis of RAPD patterns by a molecular variance method revealed that there was a high level of genetic diversity in this population and that the genetic diversity was related to plant age. Finally, we found that some of the DAPG producers, which originated from all stages of plant growth, had the same genotype. These DAPG producers could be exploited in future screening programs for biocontrol agents.

Bacterial Diversity in Spent Mushroom Compost Assessed by Amplified rDNA Restriction Analysis and Sequencing of Cultivated Isolates

2004 ◽  
Vol 27 (6) ◽  
pp. 746-754 ◽  
Author(s):  
Spyridon Ntougias ◽  
Georgios I. Zervakis ◽  
Nektarios Kavroulakis ◽  
Constantinos Ehaliotis ◽  
Constantinos Ehaliotis ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Restriction Analysis ◽  
Mushroom Compost ◽  
Spent Mushroom Compost ◽  
Amplified Rdna Restriction Analysis
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