Microbial 16S rDNA diversity in an anaerobic digester

1997 ◽  
Vol 36 (6-7) ◽  
pp. 49-55 ◽  
Author(s):  
Jean-Jacques Godon ◽  
Emmanuelle Zumstein ◽  
Patrick Dabert ◽  
Frédéric Habouzit ◽  
René Moletta
Keyword(s):  
Phylogenetic Analysis ◽  
Community Structure ◽  
16S Rdna ◽  
Bacterial Community Structure ◽  
Bacterial Population ◽  
Pcr Amplification ◽  
Operational Taxonomic Unit ◽  
Fluidized Bed Reactor ◽  
Rdna Sequences ◽  
Rdna Clone

The bacterial community structure of a fluidized bed reactor fed by vinasses was analysed by molecular identification. After PCR amplification, three 16S rDNA clone libraries of Bacteria, Archaea, and Procarya populations were established. Community structure was determined by phylogenetic analysis of 556 partial rDNA sequences (about 500 bp long). 139 OTUs (Operational Taxonomic Unit) were found among which 133 and 6 were from the Bacteria and Archaea domains respectively. The majority of bacterial OTUs are not closely related to all other hitherto-determined sequences. The ratio Archaea/Bacteria is 1/4 and the most frequent bacterial OTU represents less than 5% of the characterised bacterial population.

scholarly journals A Multiplex-PCR Method for Strain Identification and Detailed Phylogenetic Analysis of AY-Group Phytoplasmas

Plant Disease ◽  
2014 ◽  
Vol 98 (3) ◽  
pp. 299-305 ◽  
Author(s):  
Shigeyuki Kakizawa ◽  
Yoichi Kamagata
Keyword(s):  
Phylogenetic Analysis ◽  
Multiplex Pcr ◽  
16S Rdna ◽  
Pathogenic Bacteria ◽  
Target Genes ◽  
Direct Sequencing ◽  
Pcr Amplification ◽  
Single Copy ◽  
Strain Identification ◽  
Specific Detection

Phytoplasmas are plant pathogenic bacteria that cause devastating losses in the yield of diverse crops worldwide. Specific detection and strain identification of phytoplasmas is important to prevent the spread of phytoplasma-induced diseases. Hence, methods to rapidly detect these organisms are important for pest control. Polymerase chain reaction (PCR) methods using phytoplasma-specific primers are widely used to detect phytoplasmas from infected plants and insects because they are highly sensitive, easily handled, and have a variety of analytical secondary applications. The phytoplasma 16S rDNA was widely used as a target of the PCR detection method; however, further target genes and more rapid methods have been required for more specific detection of phytoplasmas. Here, we developed a multiplex-PCR system to amplify several phytoplasma genes. We designed 36 primers, based on the genome sequence of ‘Candidatus Phytoplasma asteris’, to amplify 18 single-copy genes covering wide regions of the phytoplasma genome. Nine genes could be simultaneously amplified in a single PCR. This multiplex-PCR was applied to DNAs from 10 phytoplasma strains belonging to the AY-group, and different amplification patterns were obtained between strains, suggesting that this method would allow us to differentiate phytoplasmas at the strain level. Direct sequencing was also possible after the multiplex-PCR amplification by a modified sequencing method. Detailed phylogenetic analysis was performed using concatenated sequences, and evolutionary relationships among four Japanese isolates were revealed, where these strains could not be distinguished by their 16S rDNA. Thus, this multiplex-PCR system is useful for rapid strain identification and detailed phylogenetic analysis of phytoplasmas.

scholarly journals Bacterial Community Structure and Diversity in a Century-Old Manure-Treated Agroecosystem

2004 ◽  
Vol 70 (10) ◽  
pp. 5868-5874 ◽  
Author(s):  
H. Y. Sun ◽  
S. P. Deng ◽  
W. R. Raun
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Management Practices ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
Lime Treatment ◽  
Soil Microbial Community Structure ◽  
Treated Soil

ABSTRACT Changes in soil microbial community structure and diversity may reflect environmental impact. We examined 16S rRNA gene fingerprints of bacterial communities in six agroecosystems by PCR amplification and denaturing gradient gel electrophoresis (PCR-DGGE) separation. These soils were treated with manure for over a century or different fertilizers for over 70 years. Bacterial community structure and diversity were affected by soil management practices, as evidenced by changes in the PCR-DGGE banding patterns. Bacterial community structure in the manure-treated soil was more closely related to the structure in the untreated soil than that in soils treated with inorganic fertilizers. Lime treatment had little effect on bacterial community structure. Soils treated with P and N-P had bacterial community structures more closely related to each other than to those of soils given other treatments. Among the soils tested, a significantly higher number of bacterial ribotypes and a more even distribution of the bacterial community existed in the manure-treated soil. Of the 99 clones obtained from the soil treated with manure for over a century, two (both Pseudomonas spp.) exhibited 100% similarity to sequences in the GenBank database. Two of the clones were possible chimeras. Based on similarity matching, the remaining 97 clones formed six major clusters. Fifty-six out of 97 were assigned taxonomic units which grouped into five major taxa: α-, β-, and γ-Proteobacteria (36 clones), Acidobacteria (16 clones), Bacteroidetes (2 clones), Nitrospirae (1 clone), and Firmicutes (1 clone). Forty-one clones remained unclassified. Results from this study suggested that bacterial community structure was closely related to agroecosystem management practices conducted for over 70 years.

Analysis of Bacterial Community Structure using 16S rDNA Analysis

Anaerobe ◽  
2000 ◽  
Vol 6 (2) ◽  
pp. 129-131 ◽  
Author(s):  
Bruce F. Moffett ◽  
Kerry A. Walsh ◽  
Jim A. Harris ◽  
Tom C.J. Hill
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rdna ◽  
Bacterial Community Structure ◽  
16S Rdna Analysis ◽  
Rdna Analysis

Molecular identification of Helicobacter DNA present in human colorectal adenocarcinomas by 16S rDNA PCR amplification and pyrosequencing analysis

2005 ◽  
Vol 54 (11) ◽  
pp. 1031-1035 ◽  
Author(s):  
Niclas Grahn ◽  
Mounira Hmani-Aifa ◽  
Karin Fransén ◽  
Peter Söderkvist ◽  
Hans-Jürg Monstein
Keyword(s):  
16S Rdna ◽  
Dna Sequences ◽  
Pcr Amplification ◽  
Limited Information ◽  
Rdna Sequences ◽  
Biopsy Specimens ◽  
16S Rdna Pcr ◽  
H Pylori ◽  
Species Specific ◽  
Pyrosequencing Analysis

Seroepidemiological studies have indicated that Helicobacter pylori infection might be a possible risk factor for colorectal adenocarcinoma (CRC) development. However, limited information is available as to whether or not Helicobacter species are present in CRC tissues. In this study the presence of Helicobacter DNA in 77 CRC biopsies was investigated by means of a Helicobacter species-specific 16S rDNA PCR assay and real-time DNA pyrosequencing of the 16S rDNA variable V3 region. Pyrosequencing revealed the presence of Helicobacter DNA sequences in 21 of 77 biopsy specimens (27 %). 16S rDNA sequences corresponding to H. pylori 26695 and H. pylori J99 were most commonly found. Intriguingly, one sequence belonged to Helicobacter mustelae, previously identified in ferrets. No significant correlations were found in the prevalence of Helicobacter DNA between colon and rectum tumour biopsies (P = 0.815), nor between Dukes’ classes A/B and C/D (P = 0.262). 16S rDNA PCR amplification combined with pyrosequencing analysis of 16S rDNA variable V3 regions provides a powerful molecular tool to identify Helicobacter species in human biopsy specimens.

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