Tufa microbial diversity revealed by 16S rRNA cloning in Taroko National Park, Taiwan

Ng, Chang-Chai; Huang, Wen-Chin; Chang, Chen-Chin; Tzeng, Wen-Sheng; Chen, Tseng-Wei; Liu, Yushan; Shyu, Yuan‐Tay

doi:10.1016/j.soilbio.2005.05.026

Cited by 14 publications

(12 citation statements)

References 19 publications

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“…1). Similar methods such as restriction fragment length polymorphism (RFLP), Ng et al [25] using RFLP to screening clones with different rRNA insertions. Additional, Liu et al [26] compared sensitivity of DGGE and RFLP method to resolve rRNA fragments with different sequence.…”

Section: Discussionmentioning

confidence: 99%

“…White colonies were selected and plated on LB agar plate with the antibiotic Ampicillin at a concentration of 50 µg/ml. Colony-PCR was done by using primer pair TAF (5′-CAAGGCGATTAAGTTGGGTA-3′) and TAR (5′-GGAATTGTGAGCGATAACA-3') [25] provide by the pGEM ® -T Vector Systems followed the PCR conditions described as manufacturer's manual.…”

Section: Amplification and Sequencing Of The 16s Rrna Genementioning

confidence: 99%

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Microbial diversity analysis of former salterns in southern Taiwan by 16S rRNA‐based methods

Wang

Chen

et al. 2007

J. Basic Microbiol.

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The microbiota diversity of the former salterns in southern Taiwan was investigated by denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH). Soil samples from three salterns were analyzed using DGGE and 16S rRNA from 502 colonies representing 5 archaea and 18 bacteria taxonomic groups. Each representative taxonomic group was further identified, whereas 8.7% of clones were unclassified microorganisms. Chromohalobacter, Halomonas and Virgibacillus are dominant in the Biemen saltern, Chiguensis saltern and Szutsau saltern, respectively. During FISH analysis, several taxonomic-specific probes were used. The DAPI-stained-cell count in the Szutsao saltern had a higher number of microorganisms (4.58 x 10(7) cell/cm(3)) than the other salterns. Archaea occupied 2.7-6.6% whereas bacteria accounted for 37.2-52.9% of total microbial population at the three sites. Among these three sampling sites, the Szutsao saltern had the highest diversity in halophilic microbial composition, as indicated by DGGE and FISH.

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Section: Discussionmentioning

confidence: 99%

Section: Amplification and Sequencing Of The 16s Rrna Genementioning

confidence: 99%

Microbial diversity analysis of former salterns in southern Taiwan by 16S rRNA‐based methods

Wang

Chen

et al. 2007

J. Basic Microbiol.

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“…Glucose standard was used to plot the standard curve. Measurement of glucose released from CMC was expressed as Unit (U), in which, U = mg of glucose equivalents released min -1 mL -1 crude enzyme The genomic DNA of the samples was extracted by method described by Ng et al (2006). The total 16S rRNA was amplified by primers BSF8 (52 -AGAGTTTGATCCTGGC TCAG-32 ) and BSF1507 (52 -TACCTTGTTACGACTT-32 ) (Ribosomal Database Project II).…”

Section: Methodsmentioning

confidence: 99%

Activity of cellulase from Thermoactinomycetes and Bacillus spp. isolated from Brassica waste compost

Chang

Wang

et al. 2009

Sci. agric. (Piracicaba, Braz.)

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Plant wastes present a high cellulose content, which is an ideal organic material for composting. Five strains of thermophiles from processed Brassica waste were isolated, and the hydrolytic activity on various cellulosic biomass substrata and their temperature profiles were determined. 16S rRNA sequencing identified these strains as Thermoactinomyces and Bacillus spp. Maximal cellulase activity corresponded to 2.3 U mL -1 of enzyme. The application of these strains on Brassica rapa residues demonstrates increased total nitrogen content). TA-3, a Thermoactinomycetes sp. strain, performs best among all inoculants, increasing the nitrogen content from 0.74 to 0.91%, and decreasing the carbon content from 15.4 to 12.2%, showing its high efficiency and bioactivity during compositing. Key words: cellulose degrading, enzymes, vegetable wastes ATIVIDADE DE CELULASE DE TERMOACTINOMICETOS E BACILLUS spp. ISOLADOS DE RESÍDUOS DERIVADOS DE COMPOSTOS DE BRASSICARESUMO: Resíduos vegetais apresentam alta concentração de celulose, que é um material orgânico ideal para preparação de composto. Cinco linhagens de termófilos foram isoladas de resíduos processados de Brassica e a atividade hidrolítica em vários substratos contendo celulose e seus padrões de temperatura foram determinados. O seqüenciamento de rRNA 16S permitiu a identificação dessas isolados como Thermoactinomyces e Bacillus spp. A atividade máxima de celulase foi determinada como de 2,3 U mL -1 de enzima. O uso dessas linhagens em resíduos de Brassica rapa resultou em um aumento total do conteúdo de nitrogênio. TA-3, uma linhagem de Thermoactinomycetes sp., apresentou melhor desempenho entre os inoculantes, aumentando o conteúdo de nitrogênio de 0,74 para 0,91%, e diminuindo o conteúdo de carbono de 15,4 para 12,2%, mostrando sua alta eficiência e bioatividade durante a compostagem. Palavras-chaves: degradação de celulose, enzimas, resíduos vegetais

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“…The latter three studies were based solely upon the morphological observation of microorganisms. Tufa sites investigated using molecular methods (Neilan et al 2002;Ng et al 2006) detected more cyanobacterial diversity than observed by morphology. Ng et al (2006) evaluated the 16S rRNA gene clone libraries of three core samples located in rivers flowing in the Taroko National Park, Taiwan, influenced by a subtropical monsoonal climate.…”

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confidence: 97%

“…Tufa sites investigated using molecular methods (Neilan et al 2002;Ng et al 2006) detected more cyanobacterial diversity than observed by morphology. Ng et al (2006) evaluated the 16S rRNA gene clone libraries of three core samples located in rivers flowing in the Taroko National Park, Taiwan, influenced by a subtropical monsoonal climate. Besides cyanobacteria they found a relatively diverse assemblage of heterotrophic bacteria at the genus level corresponding to only 10 phylotypes using DNA isolated from homogenized core samples.…”

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confidence: 97%

Spatial Bacterial Diversity in a Recent Freshwater Tufa Deposit

Cousin

Stackebrandt

2010

Geomicrobiology Journal

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16S ribosomal RNA gene clone libraries were generated to assess the prokaryotic diversity within a laminated tufa stromatolite core, obtained from the hardwater rivulet Westerhöfer Bach, Lower Saxony, Germany. Libraries were obtained from the biofilm and six tufa layers, each about 4 to 8 mm thick and 2,351 partial sequences were analyzed. Cyanobacteria and other aerobic organisms dominated the 500 µm thick biofilm and the first layer, represented by 112 and 154 phylotypes, respectively. DGGE and UniFrac analyses revealed that these two layers were clearly separated from the deeper layers which showed a higher diversity than the tufa surface with less than 350 phylotypes. The species richness of deeper layers was dominated by a broad range of phyla, predominantly of acidobacterial, bacteroidetes and alpha-, beta-and gammaproteobacterial phylotypes. In total, sequences belonging to 26 phyla were detected. Sequences related to anaerobes, including photosynthetic Proteobacteria, are present in low numbers in the deeper layers but their metabolic activities in the dark and water-aerated core remain unclear.Keywords biofilm, community structure, subsurface microbiology Microbialites are organo-sedimentary structures that can be formed under the influence of a variety of metabolically distinct taxa. These structures have been named stromatolites by Kalkowsky (1908) to define microbialites characterized by laminated deposits of calcium carbonate. Most studies on the participation of microorganisms in stromatolite formation concentrate on marine stromatolites as major study objects, due to their homology with Precambrian and Proterozoic analogues (Díez

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Tufa microbial diversity revealed by 16S rRNA cloning in Taroko National Park, Taiwan

Cited by 14 publications

References 19 publications

Microbial diversity analysis of former salterns in southern Taiwan by 16S rRNA‐based methods

Microbial diversity analysis of former salterns in southern Taiwan by 16S rRNA‐based methods

Activity of cellulase from Thermoactinomycetes and Bacillus spp. isolated from Brassica waste compost

Spatial Bacterial Diversity in a Recent Freshwater Tufa Deposit

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