Microbial diversity in lake sediments detected by PCR-DGGE

Abstract

In this study, PCR-denaturing gradient gel electrophoresis (DGGE) was applied to analyze the microbial communities in lake sediments from Lake Xuanwu, Lake Mochou in Nanjing and Lake Taihu in Wuxi. Sediment samples from seven locations in three lakes were collected and their genomic DNAs were extracted. The DNA yields of the sediments of Lake Xuanwu and Lake Mochou were high (10 mg/g), while that of sediments in Lake Taihu was relatively low. After DNA purification, the 16S rDNA genes (V3 to V5 region) were amplified and the amplified DNA fragments were separated by parallel DGGE. The DGGE profiles showed that there were five common bands in all the lake sediment samples indicating that there were similarities among the populations of microorganisms in all the lake sediments. The DGGE profiles of Lake Xuanwu and Lake Mochou were similar and about 20 types of microorganisms were identified in the sediment samples of both lakes. These results suggest that the sediment samples of these two city lakes (Xuanwu, Mochou) have similar microbial communities. However, the DGGE profiles of sediment samples in Lake Taihu were significantly different from these two lakes. Furthermore, the DGGE profiles of sediment samples in different locations in Lake Taihu were also different, suggesting that the microbial communities in Lake Taihu are more diversified than those in Lake Xuanwu and Lake Mochou. The differences in microbial diversity may be caused by the different environmental conditions, such as redox potential, pH, and the concentrations of organic matters. Seven major bands of 16S rDNA genes fragments from the DGGE profiles of sediment samples were further re-amplified and sequenced. The results of sequencing analysis indicate that five sequences shared 99%-100% homology with known sequences (Bacillus and Brevibacillus, uncultured bacteria), while the other two sequences shared 93%-96% homology with known sequences (Acinetobacter, and Bacillus). The study shows that the PCR-DGGE technique combined with sequence analysis is a feasible and efficient method for the determination of microbial communities in sediment samples.

Molecular characterization of soil microorganisms: effect of industrial pollution on distribution and biodiversity

“…Moreover, being pathogenic members of the coliform bacteria, they pose a real public health risk through direct contact with this soil or the crops produced from it. These results are consistent with those of Joynt et al (2006), Zhao et al (2006) and Mocali et al (2008) where pollution shifted the indigenous population to more resistant Gram-positive species mainly Bacillus and Brevibacillus ([83%) as well as Acinetobacter. In contrast to Mocali et al (2008), in the present study the dominant identified species were Gram-negative, non-spore-forming bacteria which confirmed that their dominance and resistance resulted from selective pressure of microbial species with a set of genes involved in biodegradation of such contaminants and their ability to use them as energy sources.…”

“…The PCR-DGGE or PCR-DHPLC (as in the present study) techniques combined with sequence analysis are a feasible and efficient method for the determination of microbial communities in environmental samples and differentiation of the very closely related species (Zhao et al 2006;Mocali et al 2008;Wang et al 2008;Yin et al 2008;Zhang et al 2008). However, it is obvious that due to the hazardous effect of pollution, only a low percentage of the microbial population is cultivable.…”

“…It represents an accurate, effective and fast technology for identification of microbial diversity in different environments (Ogram et al 1987;Pace 1997;Hatamoto et al 2008). Genetic diversity can identify individual organisms from some unique part of their DNA or RNA providing definitive information on soil biodiversity (Ward et al 1990;Zhao et al 2006;Betancourt et al 2008;Hatamoto et al 2008;Mocali et al 2008;Norton et al 2008;Sallam and Steinbüchel 2008;Wang et al 2008) and has also been recognized for its economic potential through bio-prospecting (Franco and McClure 1998).…”

Bacterial community structure analysis of sediment in the Sagami River, Japan using a rapid approach based on two-dimensional DNA gel electrophoresis mapping with selective primer pairs

“…For the assessment of sediment environmental stress, bacterial community may be function as indicator organisms because sediment provides substrate for bacterial colonization and nutrients for bacterial growth (Atlas 1984;Kassen and Rainey 2000;Kemp and Aller 2004;Kostanjšek et al 2005). In the recent years, molecular biological tools like denaturing gradient gel electrophoresis (DGGE) and temporal temperature gradient electrophoresis (TTGE) have become popular for bacterial community analysis in sediments due to their effectivity to monitor bacterial structure changes (Torsvik et al 2002;Freitag and Prosser 2003;Kostanjšek et al 2005;Zhao et al 2008;Ikenaga et al 2009). The methodological protocols are mainly based on sequencing analyses of 16S ribosomal DNA (rDNA) fragments from dominant electrophoresed bands on a gel.…”

Presence of indigenous endophytic bacteria in jujube seedlings germinated from seeds in vitro

“…Moreover, a brighter band signal suggested a higher richness of the species. Therefore, we could obtain information about the number of dominant species and quantity of microbes in the samples (Zhao et al, 2008). The DGGE patterns were showed in Fig.…”