Monitoring impact of in situ biostimulation treatment on groundwater bacterial community by DGGE

Iwamoto, Tomotada; Tani, Katsuji; Nakamura, Kanji; Suzuki, Yoshio; Kitagawa, Masayoshi; Eguchi, M.; Nasu, Masao

doi:10.1111/j.1574-6941.2000.tb00707.x

Cited by 214 publications

(119 citation statements)

References 61 publications

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“…Thus, this simple method is suitable for analyzing many samples simultaneously. TaqGold is often used for PCR amplification of eubacterial 16S rRNA genes from freshwater samples 10,11,14,15) ; however, this DNA polymerase was not very effective in our study.…”

Section: Resultscontrasting

confidence: 43%

“…Bacterial populations in both eutrophic (e.g., canal and river) and oligotrophic (e.g., tap water) aquatic environments could be analyzed by the optimized PCR-DGGE procedure. DGGE is suitable to detect changes in microbial communities caused by human activities, 15) and temporally and spatially continuous analyses of bacterial populations in Bangkok canals and rivers by PCR-DGGE should be useful to recognize disturbances in microbial ecosystems caused by excess inflow of wastewater.…”

Section: Resultsmentioning

confidence: 99%

“…15) Bacterial cells in water samples were vacuum-filtered onto polycarbonate white filters (pore size: 0.2 µm). In the simple freeze-thaw method, these filters were placed into sterilized tubes with 400 µl of sterile DNA-free water.…”

Section: Sampling Sitesmentioning

confidence: 99%

“…15) For DGGE analysis of the PCR products, a GC-clamp (5′-CGC CCG CCG CGC GCG GCG GGC GGG GCG GGG GCA CGG GGG G-3′) was attached to the 5′ end of primer EUB f933. PCR was performed with one of the following enzymes according to the manufacturer's guidelines: Ampli Taq Gold (Applied Biosystems, Foster City, CA, U.S.A.), lA Taq (TaKaRa Bio, Shiga, Japan), rTaq (Toyobo, Osaka, Japan), KOD Plus (Toyobo), or Platinum Pfx (Invitrogen, Carlsbad, CA, U.S.A.).…”

Section: Sampling Sitesmentioning

confidence: 99%

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16S Ribosomal RNA Gene-Based Phylogenetic Analysis of Abundant Bacteria in River, Canal and Potable Water in Bangkok, Thailand

Yamaguchi

Nishiguchi

Utrarachkij

et al. 2013

Biological & Pharmaceutical Bulletin

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In Southeast Asian countries, industrialization and urbanization is occurring rapidly, and water pollution in rivers and canals poses serious problems in some areas, especially in cities. Excess inflow of domestic, agricultural, and industrial wastewater to freshwater environments disturbs the aquatic microbial ecosystem, which can further pollute water by inhibiting biodegradation of pollutants. Therefore, monitoring of microbes in freshwater environment is important to identify changes in indigenous microbial populations and to estimate the influence of wastewater inflows on them. Polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) analysis is suitable for monitoring changes in microbial communities caused by human activities, but this method can be difficult in eutrophic freshwater samples that contain PCR inhibitors. In this study, we optimized DNA extraction procedures and PCR conditions for DGGE analysis of bacterial populations in freshwater samples (canal, river, and tap water) collected in Bangkok, Thailand. A simple freeze-thaw procedure was effective for extracting DNA from bacterial cells in the samples, and LA Taq with added bovine serum albumin provided the best PCR amplification. The PCR-DGGE approach revealed that the most common bacteria in freshwater samples belonged to Gammaproteobacteria, while a Gram-positive bacterium was present at Bangkok Noi Canal. Temporally and spatially continuous analyses of bacterial populations in Bangkok canals and rivers by PCR-DGGE approach should be useful to recognize disturbances of microbial ecosystems caused by excess inflows of wastewater.

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Section: Resultscontrasting

confidence: 43%

Section: Resultsmentioning

confidence: 99%

Section: Sampling Sitesmentioning

confidence: 99%

Section: Sampling Sitesmentioning

confidence: 99%

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16S Ribosomal RNA Gene-Based Phylogenetic Analysis of Abundant Bacteria in River, Canal and Potable Water in Bangkok, Thailand

Yamaguchi

Nishiguchi

Utrarachkij

et al. 2013

Biological & Pharmaceutical Bulletin

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“…were isolated and identified by biochemical tests and fatty acid methyl ester analysis (FAME). These included B. pumilus (16) (1) and Bacillus GC group 22 (1). The Bacillus GC group 22 corresponds to the gas chromatographic profile of a Bacillus species in the Sherlock TSBA Library version 3.9 (Microbial ID, MIDI Inc.), the 16S rDNA sequence of which does not match any known species of the genus Bacillus.…”

Section: Taxonomic Identification Of Bacillus Spp Isolated From Coasmentioning

confidence: 99%

Biochemical and molecular characterization of Bacillus pumilus isolated from coastal environment in Cochin, India

Parvathi¹,

Krishna²,

Jose³

et al. 2009

Braz. J. Microbiol.

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Bacillus species constitute a diverse group of bacteria widely distributed in soil and the aquatic environment. In this study, Bacillus strains isolated from the coastal environment of Cochin, India were identified by detailed conventional biochemical methods, fatty acid methyl ester (FAME) analysis and partial 16S rDNA sequencing. Analysis of the data revealed that Bacillus pumilus was the most predominant species in the region under study followed by B. cereus and B. sphaericus. The B. pumilus isolates were further characterized by arbitrarily primed PCR (AP-PCR), antibiotic sensitivity profiling and PCR screening for known toxin genes associated with Bacillus spp. All B. pumilus isolates were biochemically identical, exhibited high protease and lipase activity and uniformly sensitive to antibiotics tested in this study. One strain of B. pumilus harboured cereulide synthetase gene cesB of B. cereus which was indistinguishable from rest of the isolates biochemically and by AP-PCR. This study reports, for the first time, the presence of the emetic toxin gene cesB in B. pumilus.

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Methanotrophic Bacteria

Graham

Kim

Lindner

2003

Encyclopedia of Environmental Microbiology

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Monitoring impact of in situ biostimulation treatment on groundwater bacterial community by DGGE

Cited by 214 publications

References 61 publications

16S Ribosomal RNA Gene-Based Phylogenetic Analysis of Abundant Bacteria in River, Canal and Potable Water in Bangkok, Thailand

16S Ribosomal RNA Gene-Based Phylogenetic Analysis of Abundant Bacteria in River, Canal and Potable Water in Bangkok, Thailand

Biochemical and molecular characterization of Bacillus pumilus isolated from coastal environment in Cochin, India

Methanotrophic Bacteria

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