[Show abstract][Hide abstract] ABSTRACT: Two acid mine drainage (AMD) samples TS and WK, which were from the Dachang metals-rich mine in Guangxi province, China, were studied using PCR-based cloning approach. A total of 44 operational taxonomic units (OTUs) were obtained from the two AMD samples. However, only three OTUs (GXDC-9, GXDC-19 and GXDC-50) detected in sample TS can also be observed in sample WK. Phylogenetic analysis revealed that the bacteria in the two samples fell into four putative divisions, which were Nitrospira, Alphaproteobacteria, Gamaproteobacteria, and Acidobacteria. Organisms of genuses Acidithiobacillus and Leptospirillum, which were in gamaproteobacteria class and Nitrospira family, were dominant in two samples, respectively. In sample TS, which was characterized by low pH, high sulfate, high iron, and high arsenide, two species (Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans) constituted 98.22% of the entire microbial community. Compared with sample TS, the microbial community in sample WK was more diversified according to the observation. Interestedly, the Legionella species, which was rarely observed in the low-pH environment, was detected in sample WK. This work helps us to further understand the diversity of microbial community living in extreme acid mine drainages with unique geochemistry and the tolerance capability of acidophiles to heavy metal.
Transactions of Nonferrous Metals Society of China 06/2010; · 1.00 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: There is an urgent need for early sex identification to support field planting in Ginkgo biloba L., due to the different economic and medicinal values between male and female trees. An easy, rapid and reliable molecular
method for sex type determination of G. biloba was reported in the paper. Random amplification of polymorphic DNA (RAPD) and sequence-characterized amplified region (SCAR)
were used to search for specific molecular markers linked to the sex locus. A total of 48 primers were used for screening of specific RAPD markers in six male and three female samples. Only one primer,
S10, showed different amplification band patterns associated with sex types. Then the sex-specific bands, S10-BandA and S10-BandB,
were cloned and sequenced. Based on the sequences two pairs of SCAR primers, GBA and GBB, were designed. The GBA primers amplify
a single 571bp band in male samples but not in female samples, and DNA amplification using GBB primers could generate a 688bp
band only in the female individuals. Finally, the SCAR primers were used to test 16 sex-unknown samples. SCAR primers developed
in this paper can be used as effective, convenient and reliable molecular markers for sex identification in G. biloba.
[Show abstract][Hide abstract] ABSTRACT: Micro-array based genomic technology provides the high-throughput advantages for comprehensive understanding of complex microbial communities. In the present study, a community genome array (CGA) has been developed and evaluated for bacterial detection and microbial community analysis of acid mine drainage and bioleaching systems. This array contains 51 probes from pure culture prokaryotic whole genomic DNA. Based on the results of micro-array hybridization, specificity tests with representative pure cultures indicated that the probes on the arrays appeared to be specific to their corresponding target genomic DNA. Cross-hybridization occurred between strains of the same species, but little cross-hybridization was observed among different species. The detection limit was estimated to be approximately 0.2 ng with genomic DNA from a single pure culture bacterial and 5 ng with mixed genomic DNA from mixtures of known amounts of different species' genomic DNA. In addition, strong linear relationships were observed between hybridization signal intensity and the target DNA concentrations for pure cultures and a mixture of DNA template (r2=0.95 to 0.985). Application of this type of the micro-array revealed the differences in microbial community composition. The results indicate that this technology has potential as a specific, sensitive and quantitative tool for detection and identification of acidophilic microorganism and the microbial community in acid mine drainage and bioleaching systems.
[Show abstract][Hide abstract] ABSTRACT: The diversity of bacterial communities at three sites impacted by acid mine drainage (AMD) from the Yinshan Mine in China was studied using comparative sequence analysis of two molecular markers, the 16S rRNA and gyrB genes. The phylogenetic analyses retrieved sequences from six classes of bacteria, Nitrospira, Alphaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Acidobacteria, and Actinobacteria, as well as sequences related to the plastid of the cyanobacterium Cyanidium acidocaldarium and also some unknown bacteria. The results of phylogenetic analyses based on gyrB and 16S rRNA were compared. This confirmed that gyrB gene analysis may be a useful tool, in addition to the comparative sequence analysis of the 16S rRNA gene, for the analysis of microbial community compositions. Moreover, the Mantel test showed that the geochemical characteristics, especially the pH value and the concentration of iron, strongly influenced the composition of the microbial communities.
Systematic and Applied Microbiology 08/2008; 31(4):302-11. · 3.31 Impact Factor