16S rDNA library-based analysis of ruminal bacterial diversity

Studies on the impact of Eucalyptus spp. on Brazilian soils have focused on soil chemical properties and isolating interesting microbial organisms. Few studies have focused on microbial diversity and ecology in Brazil due to limited coverage of traditional cultivation and isolation methods. Molecular microbial ecology methods based on PCR amplified 16S rDNA have enriched the knowledge of soils microbial biodiversity. The objective of this work was to compare and estimate the bacterial diversity of sympatric communities within soils from two areas, a native forest (NFA) and an eucalyptus arboretum (EAA). PCR primers, whose target soil metagenomic 16S rDNA were used to amplify soil DNA, were cloned using pGEM-T and sequenced to determine bacterial diversity. From the NFA soil 134 clones were analyzed, while 116 clones were analyzed from the EAA soil samples. The sequences were compared with those online at the GenBank. Phylogenetic analyses revealed differences between the soil types and high diversity in both communities. Soil from the Eucalyptus spp. arboretum was found to have a greater bacterial diversity than the soil investigated from the native forest area.

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Molecular bacterial diversity and distribution in waste from a steel plant

Canadian Journal of Microbiology ◽

10.1139/w08-094 ◽

2008 ◽

Vol 54 (12) ◽

pp. 996-1005 ◽

Cited By ~ 4

Author(s):

Dulcecleide B. Freitas ◽

Mariana P. Reis ◽

Leandro M. Freitas ◽

Paulo S. Assis ◽

Edmar Chartone-Souza ◽

...

Keyword(s):

Bacterial Diversity ◽

16S Rdna ◽

Bacterial Communities ◽

Sequence Similarity ◽

Diversity Indices ◽

Operational Taxonomic Units ◽

Rdna Sequences ◽

Partial Length ◽

16S Rdna Sequences ◽

Novel Taxa

We characterized the bacterial diversity of newly produced steelmaking wastes (NPSW) and steelmaking wastes deposited (SWD) in a restricted land area, generated by the siderurgic industry, using the 16S rDNA clone library approach. A total of 212 partial-length sequences were analyzed, revealing 123 distinct operational taxonomic units (OTUs) determined by the DOTUR program to 97% sequence similarity. Phylogenetic analysis of bacterial 16S rDNA sequences from the NPSW and SWD libraries demonstrated that Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, Actinobacteria, Planctomycetes, Firmicutes, and Bacteroidetes were represented in both libraries. Deltaproteobacteria, Acidobacteria, Chloroflexi, Deinococcus-thermus, Gemmatimonadetes, and candidate divisions OP10 and OD1 were only present in the SWD library, and Nitrospira was only present in the NPSW library. The abundance of sequences affiliated with Gammaproteobacteria was high in both libraries. Six previously unclassified OTUs may represent novel taxa. Based on diversity indices (Simpson, Shannon–Weaver, Chao1, and ACE), the SWD library had a higher diversity. LIBSHUFF comparisons of the composition of the 2 libraries showed that they were significantly different. These results indicate that the bacterial communities in steelmaking wastes present high phylogenetic diversity and complexity. A possible association between the functional diversity and the bacterial communities’ complexity requires further phenotypic investigation.

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Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis.

The FASEB Journal ◽

10.1096/fasebj.7.1.8422969 ◽

1993 ◽

Vol 7 (1) ◽

pp. 232-236 ◽

Cited By ~ 172

Author(s):

E Stackebrandt ◽

W Liesack ◽

B M Goebel

Keyword(s):

Soil Sample ◽

Bacterial Diversity ◽

16S Rdna ◽

16S Rdna Analysis ◽

Rdna Analysis

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Assessment of bacterial diversity in selected Philippine fermented food products through PCR-DGGE

Beneficial Microbes ◽

10.3920/bm2011.0017 ◽

2011 ◽

Vol 2 (4) ◽

pp. 273-281 ◽

Cited By ~ 11

Author(s):

L.M. Dalmacio ◽

A.K. Angeles ◽

L.L. Larcia ◽

M. Balolong ◽

R. Estacio

Keyword(s):

Bacterial Diversity ◽

16S Rdna ◽

Denaturing Gradient Gel Electrophoresis ◽

Acetic Acid Bacteria ◽

Food Samples ◽

Fermented Food ◽

Probiotic Bacteria ◽

Rrna Gene ◽

Fermented Foods ◽

16S Rdna Pcr

The bacterial population in several Philippine fermented food preparations was assessed by PCR-denaturing gradient gel electrophoresis (PCR-DGGE) of the 16S rRNA gene (16S rDNA). Genomic DNA was isolated directly from alamang (fermented shrimp paste), burong isda (fermented fish and rice), burong hipon (fermented shrimp and rice), burong mustasa (fermented mustard leaves), tuba (sugar cane wine), suka (vinegar) and sinamak (spiced vinegar) using one of two protocols, namely – MoBio DNA Extraction Kit procedure and a cetyltrimethylammonium bromide-based method. Samples recalcitrant to both methods underwent enrichment in three culture broths prior to DNA isolation. Isolated DNA was amplified using nested primer pairs targeting the bacterial 16S rDNA. PCR products were subjected to DGGE to elucidate the bacterial diversity in each fermented food. 16S rDNA sequence analyses revealed that lactic acid bacteria (LAB) and acetic acid bacteria (AAB) were dominant in the food samples. The LAB identified were Lactobacillus fermentum, Lactobacillus plantarum, Lactobacillus panis, Lactobacillus pontis and Weissella cibaria. Identified AAB were Acetobacter pomorum, Acetobacter ghanensis, Acetobacter orientalis, and Acetobacter pasteurianus. Among these, L. fermentum, L. plantarum and W. cibaria are established probiotic bacteria, while L. panis and L. pontis are potential probiotic bacteria. This finding would increase the appeal and significance of local fermented foods to consumers. Furthermore, the majority of the identified bacteria in the study have not been reported before in culture-dependent studies of similar food preparations. As such, some of the bacterial 16S rDNA obtained were cloned to have an initial partial bacterial 16S rDNA library for Philippine fermented foods.

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