Methanogenic archaeal communities developed in paddy fields in the Kojima Bay polder, estimated by denaturing gradient gel electrophoresis, real-time PCR and sequencing analyses

ABSTRACT The microbial flora of the vagina plays a major role in preventing genital infections, including bacterial vaginosis (BV) and candidiasis (CA). An integrated approach based on PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and real-time PCR was used to study the structure and dynamics of bacterial communities in vaginal fluids of healthy women and patients developing BV and CA. Universal eubacterial primers and Lactobacillus genus-specific primers, both targeted at 16S rRNA genes, were used in DGGE and real-time PCR analysis, respectively. The DGGE profiles revealed that the vaginal flora was dominated by Lactobacillus species under healthy conditions, whereas several potentially pathogenic bacteria were present in the flora of women with BV. Lactobacilli were the predominant bacterial population in the vagina for patients affected by CA, but changes in the composition of Lactobacillus species were observed. Real-time PCR analysis allowed the quantitative estimation of variations in lactobacilli associated with BV and CA diseases. A statistically significant decrease in the relative abundance of lactobacilli was found in vaginal fluids of patients with BV compared to the relative abundance of lactobacilli in the vaginal fluids of healthy women and patients with CA.

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Expression of thenifHgene in diazotrophic bacteria inEucalyptus urograndisplantations

Canadian Journal of Forest Research ◽

10.1139/cjfr-2015-0063 ◽

2016 ◽

Vol 46 (2) ◽

pp. 190-199 ◽

Cited By ~ 3

Author(s):

Marliane de Cássia Soares da Silva ◽

Igor Rodrigues Mendes ◽

Thiago de Almeida Paula ◽

Roberto Sousa Dias ◽

Sérgio Oliveira de Paula ◽

...

Keyword(s):

Real Time ◽

Real Time Pcr ◽

Denaturing Gradient Gel Electrophoresis ◽

Nifh Gene ◽

Root Systems ◽

N Fertilization ◽

Quantitative Real Time Pcr ◽

Diazotrophic Bacteria ◽

Eucalypt Plantations ◽

Gradient Gel Electrophoresis

A large proportion of eucalypt plantations in Brazil are located in areas with low soil fertility. The actions of microorganisms are of great importance for the cycling of nutrients, including nitrogen (N), that are essential for plant metabolism. Denaturing gradient gel electrophoresis (DGGE) was used to monitor and identify the total and active microorganisms involved in the N cycle in both the soil and root systems of a forest of Eucalyptus urograndis with sections that were fertilized with N or unfertilized. Quantitative real-time PCR was used to examine the expression of the nifH gene in N-fixing bacteria present in both the soil and root systems. According to the DGGE analysis, in the total and active populations of N-fixing bacteria, the presence and expression of the nifH gene were influenced by the winter and summer seasons and (or) N fertilization, respectively. DGGE band sequencing from total DNA samples showed that the most abundant group of diazotrophic bacteria belonged to Alphaproteobacteria in both the soil and root systems. Quantitative real-time PCR revealed that nifH expression was higher in the soil samples, especially in those that did not receive N fertilization. The differences in the composition of the total and active diazotrophic populations highlight the importance of evaluating the active populations, because they are effectively responsible for the biogeochemical transformation of N and also control its’ availability to plants.

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Diversity of methanogenic archaeal communities in Japanese paddy field ecosystem, estimated by denaturing gradient gel electrophoresis

Biology and Fertility of Soils ◽

10.1007/s00374-009-0435-2 ◽

2010 ◽

Vol 46 (4) ◽

pp. 343-353 ◽

Cited By ~ 18

Author(s):

Takeshi Watanabe ◽

Makoto Kimura ◽

Susumu Asakawa

Keyword(s):

Paddy Field ◽

Gel Electrophoresis ◽

Denaturing Gradient Gel Electrophoresis ◽

Gradient Gel Electrophoresis ◽

Field Ecosystem ◽

Archaeal Communities

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Temporal distribution of the archaeal community in the Changjiang Estuary hypoxia area and the adjacent East China Sea as determined by denaturing gradient gel electrophoresis and multivariate analysis

Canadian Journal of Microbiology ◽

10.1139/w11-037 ◽

2011 ◽

Vol 57 (6) ◽

pp. 504-513 ◽

Cited By ~ 10

Author(s):

Min Liu ◽

Tian Xiao ◽

Ying Wu ◽

Feng Zhou ◽

Wuchang Zhang

Keyword(s):

East China Sea ◽

Gel Electrophoresis ◽

Denaturing Gradient Gel Electrophoresis ◽

Archaeal Community ◽

Changjiang Estuary ◽

East China ◽

The Changjiang Estuary ◽

China Sea ◽

Gradient Gel Electrophoresis ◽

Archaeal Communities

The archaeal community and the effects of environmental factors on microbial community distribution were investigated at five sampling sites in the Changjiang Estuary hypoxia area and the adjacent East China Sea in June, August, and October 2006. Profiles of the archaeal communities were generated by denaturing gradient gel electrophoresis of 16S rRNA genes followed by DNA sequence analysis, and the results were analyzed by multivariate statistical analysis. Denaturing gradient gel electrophoresis band patterns were analyzed by cluster analysis to assess temporal changes in the genetic diversity of the archaeal communities. Most of the October samples grouped together separately from those of June and August. Analysis of DNA sequences revealed that the dominant archaeal groups in the Changjiang Estuary hypoxia area and the adjacent East China Sea were affiliated with Euryarchaeota (mainly marine group II) and Crenarchaeota. The effects of environmental factors on the archaeal community distribution were analyzed by the ordination technique of canonical correspondence analysis. Salinity had a significant effect on the archaeal community composition.

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