Bacterial communities inside and in the vicinity of the Chinese Great Wall Station, King George Island, Antarctica

2007 ◽  
Vol 19 (1) ◽  
pp. 11-16 ◽  
Author(s):  
Xiang Xiao ◽  
Mingguang Li ◽  
Ziyong You ◽  
Fengping Wang
Keyword(s):  
Bacterial Diversity ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Heterotrophic Bacteria ◽  
Soil Samples ◽  
Rrna Gene ◽  
Adjacent Area ◽  
Molecular Approaches ◽  
Cell Counts ◽  
Two Samples ◽  
Great Wall

Both bacterial culture and molecular approaches were used to investigate the bacterial diversity inside the Chinese Antarctic Great Wall Station and in its adjacent area. Heterotrophic bacteria were isolated from the samples using a direct plating method. γ-Proteobacteria, Actinobacteria, Flavobacteria and Firmicutes were isolated from these samples. In the three water samples, Pseudomonas species were dominant. In soil samples, Flavobacterium, Bacillus or Arthrobacter species dominated. Escherichia coli strains were isolated only in two samples from inside the station. Total cell counts in the six soil samples were semi-quantified by Quantitative Competitive-PCR of the 16S rRNA gene copies. The soil samples contained 105 to 109 cells g−1. Denaturing gradient gel electrophoresis (DGGE) was used further to investigate the bacterial diversity in the soil samples. A wider range of bacterial diversity including α-Proteobacteria, β-Proteobacteria, δ-Proteobacteria, γ-Proteobacteria, Flavobacteria, Actinobacteria and unclassified bacteria was discovered.

scholarly journals Changes in Bacterial Diversity Associated with Epithelial Tissue in the Beef Cow Rumen during the Transition to a High-Grain Diet

2011 ◽  
Vol 77 (16) ◽  
pp. 5770-5781 ◽  
Author(s):  
Yanhong Chen ◽  
Gregory B. Penner ◽  
Meiju Li ◽  
Masahito Oba ◽  
Le Luo Guan
Keyword(s):  
Bacterial Diversity ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pcr Analysis ◽  
Control Group ◽  
Epithelial Tissue ◽  
Rrna Gene ◽  
Content Type ◽  
Beef Cow ◽  
Dietary Transition ◽  
Gradient Gel Electrophoresis

ABSTRACTOur understanding of the ruminal epithelial tissue-associated bacterial (defined as epimural bacteria in this study) community is limited. In this study, we aimed to determine whether diet influences the diversity of the epimural bacterial community in the bovine rumen. Twenty-four beef heifers were randomly assigned to either a rapid grain adaptation (RGA) treatment (n= 18) in which the heifers were allowed to adapt from a diet containing 97% hay to a diet containing 8% hay over 29 days or to the control group (n= 6), which was fed 97% hay. Rumen papillae were collected when the heifers were fed 97%, 25%, and 8% hay diets. PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR analysis were used to characterize rumen epimural bacterial diversity and to estimate the total epimural bacterial population (copy numbers of the 16S rRNA gene). The epimural bacterial diversity from RGA heifers changed (P= 0.01) in response to the rapid dietary transition, whereas it was not affected in control heifers. A total of 88 PCR-DGGE bands were detected, and 44 were identified from phyla includingFirmicutes,Bacteroidetes, andProteobacteria. The bacteriaTreponemasp.,Ruminobactersp., andLachnospiraceaesp. were detected only when heifers were fed 25% and 8% hay diets, suggesting the presence of these bacteria is the result of adaptation to the high-grain diets. In addition, the total estimated population of rumen epimural bacteria was positively correlated with molar proportions of acetate, isobutyrate, and isovalerate, suggesting that they may play a role in volatile fatty acid metabolism in the rumen.

PCR-DGGE Analysis of Bacterial Diversity of Intestinal System in Hyperlipidemia Rats

2013 ◽  
Vol 726-731 ◽  
pp. 898-901
Author(s):  
Ri Na Wu ◽  
Xiao Meng Pang ◽  
Xi Yan Wang ◽  
Jun Rui Wu
Keyword(s):  
Bacterial Diversity ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Intestinal Flora ◽  
Intestinal Bacteria ◽  
Control Group ◽  
Rrna Gene ◽  
Dgge Analysis ◽  
Gradient Gel Electrophoresis ◽  
The Relationship ◽  
Insight Into

Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene has been regarded as one of powerful tools for gaining insight into the bacterial diversity of intestinal system. In the present study, hyperlipidemia model was constructed in rat according to the tests of blood lipids. Fecal samples of rats were collected after 60d feeding, and DGGE was used to investigate the diversities of intestinal bacteria in the artificially-induced hyperlipidemia rats and normal rats. The results showed that two patterns had similarities, but there were also some different bacteria communities. Moreover, control group had much more bands than model group on gel, showing species in intestinal of model rats might be deduced by hyperlipidemia. It will be helpful to explore the relationship between hyperlipidemia and intestinal flora.

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

2011 ◽  
Vol 2 (4) ◽  
pp. 273-281 ◽  
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.

scholarly journals Unexpectedly High Bacterial Diversity in Arctic Tundra Relative to Boreal Forest Soils, Revealed by Serial Analysis of Ribosomal Sequence Tags

2005 ◽  
Vol 71 (10) ◽  
pp. 5710-5718 ◽  
Author(s):  
Josh D. Neufeld ◽  
William W. Mohn
Keyword(s):  
Boreal Forest ◽  
Bacterial Diversity ◽  
Forest Soils ◽  
Atmospheric Chemistry ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Arctic Tundra ◽  
Soil Samples ◽  
Arctic Soil ◽  
Gradient Gel Electrophoresis ◽  
Diversity Estimates

ABSTRACT Arctic tundra and boreal forest soils have globally relevant functions that affect atmospheric chemistry and climate, yet the bacterial composition and diversity of these soils have received little study. Serial analysis of ribosomal sequence tags (SARST) and denaturing gradient gel electrophoresis (DGGE) were used to compare composite soil samples taken from boreal and arctic biomes. This study comprises an extensive comparison of geographically distant soil bacterial communities, involving the analysis of 12,850 ribosomal sequence tags from six composite soil samples. Bacterial diversity estimates were greater for undisturbed arctic tundra soil samples than for boreal forest soil samples, with the highest diversity associated with a sample from an extreme northern location (82oN). The lowest diversity estimate was obtained from an arctic soil sample that was disturbed by compaction and sampled from a greater depth. Since samples from the two biomes did not form distinct clusters on the basis of SARST data and DGGE fingerprints, factors other than latitude likely influenced the phylogenetic compositions of these communities. The high number of ribosomal sequences analyzed enabled the identification of possible cosmopolitan and endemic bacterial distributions in particular soils.

Bacterial diversity in Philippine fermented mustard (burong mustasa) as revealed by 16S rRNA gene analysis

2011 ◽  
Vol 2 (4) ◽  
pp. 263-271 ◽  
Author(s):  
L.L. Larcia II ◽  
R. Estacio ◽  
L.M. Dalmacio
Keyword(s):  
Bacterial Diversity ◽  
16S Rdna ◽  
Nested Pcr ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Independent Study ◽  
Vector System ◽  
Rrna Gene ◽  
Bacterial Identification ◽  
16S Rrna Gene Analysis ◽  
Cloned Gene

Previous studies on the bacterial profile of burong mustasa, a traditional Philippine fermented food, had been conducted using culture-dependent techniques. Since these methods may underestimate the total microbiota of a sample, a culture-independent study was done to determine the bacterial diversity in burong mustasa through molecular biology techniques. Bacterial DNA was isolated from fermented mustard samples at different stages of fermentation. The isolated genomic DNA was amplified by PCR using specific primers for the 16S ribosomal RNA gene (16S rDNA). The 1.5 kb amplicons obtained were subjected to nested PCR using primers for the internal variable region of the 16S rDNA. The 585 bp nested PCR amplicons were then subjected to denaturing gradient gel electrophoresis (DGGE) to separate the different bacteria present in each sample. Distinct and unique bands in the DGGE profile were excised, reamplified, purified and sequenced for bacterial identification. Molecular cloning of the 1.5 kb 16S rDNA was also performed using the pGEM-T Easy Vector System. The cloned gene was sequenced for bacterial identification. The identified microbiota in burong mustasa at different stages of fermentation include lactic acid bacteria and several uncultured bacteria (initial up to the final stages); acetic acid bacteria (middle stage); and Streptobacillus and Fusobacterium species (initial stage). The potential probiotic bacteria found in burong mustasa are Weissella and Lactobacillus.

Bacterial diversity within the planktonic community of an artesian water supply

2006 ◽  
Vol 52 (3) ◽  
pp. 246-259 ◽  
Author(s):  
Christopher L Ball ◽  
Ronald L Crawford
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Water Supply ◽  
Bacterial Diversity ◽  
Cultured Cells ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Enrichment Culture ◽  
Rrna Gene ◽  
Artesian Water ◽  
Planktonic Community

Culture and molecular methods were used to describe the planktonic bacterial diversity of an artesian water supply in rural Latah County, Idaho, within the drainage of a small perennial stream, Thorn Creek. The surrounding depth to groundwater at this location is thought to be significant (>100 m), and this transitional zone (basalt–granite) of the Palouse aquifer system is little studied. The water produced by this artesian source is consistent even in years of drought and is of high quality, both mineralogically and microbiologically. A culture-based analysis using 30 media types and four incubation temperatures demonstrated that several metabolic types were present in the water. 16S rRNA gene fragments amplified from the DNA of pooled cultured cells and from the DNA extracted from 1 L of the source water were compared using denaturing gradient gel electrophoresis. The results indicated that the two DNA samples did not have similar 16S rRNA gene compositions and that several uncultured phyla were present in the community DNA sample. These results indicated that large-scale culturing did not accurately represent the structure planktonic community. 16S rRNA gene sequences from 17 different genera were obtained from the community DNA sample; the most abundant were similar to Rhodoferax, Rhodobacter, and Polaromonas species. Sequences related to the Proteo bacteria, Bacteroidetes/Chlorobi, Firmicutes, and Acidobacterium/Fibrobacter divisions were also detected.Key words: artesian spring, bacterial diversity, DGGE, 16S rRNA, enrichment culture.

scholarly journals Development and Application of a Selective PCR-Denaturing Gradient Gel Electrophoresis Approach To Detect a Recently Cultivated Bacillus Group Predominant in Soil

2004 ◽  
Vol 70 (10) ◽  
pp. 5801-5809 ◽  
Author(s):  
Vesela A. Tzeneva ◽  
Youguo Li ◽  
Andreas D. M. Felske ◽  
Willem M. de Vos ◽  
Antoon D. L. Akkermans ◽  
...  
Keyword(s):  
16S Rrna ◽  
The Netherlands ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Physiological State ◽  
Soil Samples ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Gradient Gel Electrophoresis

ABSTRACT The worldwide presence of a hitherto-nondescribed group of predominant soil microorganisms related to Bacillus benzoevorans was analyzed after development of two sets of selective primers targeting 16S rRNA genes in combination with denaturing gradient gel electrophoresis (DGGE). The high abundance and cultivability of at least some of these microorganisms makes them an appropriate subject for studies on their biogeographical dissemination and diversity. Since cultivability can vary significantly with the physiological state and even between closely related strains, we developed a culture-independent 16S rRNA gene-targeted DGGE fingerprinting protocol for the detection of these bacteria from soil samples. The composition of the B. benzoevorans relatives in the soil samples from The Netherlands, Bulgaria, Russia, Pakistan, and Portugal showed remarkable differences between the different countries. Differences in the DGGE profiles of these communities in archived soil samples from the Dutch Wieringermeer polder were observed over time during which a shift from anaerobic to aerobic and from saline to freshwater conditions occurred. To complement the molecular methods, we additionally cultivated B. benzoevorans-related strains from all of the soil samples. The highest number of B. benzoevorans relatives was found in the soils from the northern part of The Netherlands. The present study contributes to our knowledge of the diversity and abundance of this interesting group of microbes in soils throughout the world.

scholarly journals Molecular Method To Assess the Diversity of Burkholderia Species in Environmental Samples

2002 ◽  
Vol 68 (4) ◽  
pp. 1595-1603 ◽  
Author(s):  
Joana Falcão Salles ◽  
Francisco Adriano De Souza ◽  
Jan Dirk van Elsas
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Direct Method ◽  
Soil Samples ◽  
Rrna Gene ◽  
Migration Behavior ◽  
Soil Dna ◽  
Soil Microbial ◽  
Specificity And Sensitivity ◽  
Pcr Products ◽  
Gradient Gel Electrophoresis

ABSTRACT In spite of the importance of many members of the genus Burkholderia in the soil microbial community, no direct method to assess the diversity of this genus has been developed so far. The aim of this work was the development of soil DNA-based PCR-denaturing gradient gel electrophoresis (DGGE), a powerful tool for studying the diversity of microbial communities, for detection and analysis of the Burkholderia diversity in soil samples. Primers specific for the genus Burkholderia were developed based on the 16S rRNA gene sequence and were evaluated in PCRs performed with genomic DNAs from Burkholderia and non-Burkholderia species as the templates. The primer system used exhibited good specificity and sensitivity for the majority of established species of the genus Burkholderia. DGGE analyses of the PCR products obtained showed that there were sufficient differences in migration behavior to distinguish the majority of the 14 Burkholderia species tested. Sequence analysis of amplicons generated with soil DNA exclusively revealed sequences affiliated with sequences of Burkholderia species, demonstrating that the PCR-DGGE method is suitable for studying the diversity of this genus in natural settings. A PCR-DGGE analysis of the Burkholderia communities in two grassland plots revealed differences in diversity mainly between bulk and rhizosphere soil samples; the communities in the latter samples produced more complex patterns.

Bacterial diversity of soil samples from the western Himalayas, India

2009 ◽  
Vol 55 (5) ◽  
pp. 564-577 ◽  
Author(s):  
Pooja Gangwar ◽  
Syed Imteyaz Alam ◽  
Sunita Bansod ◽  
Lokendra Singh
Keyword(s):  
Bacterial Diversity ◽  
Bacterial Species ◽  
Hydrolytic Enzymes ◽  
Soil Samples ◽  
Rrna Gene ◽  
Organic Carbon Content ◽  
Western Himalayas ◽  
Bacterial Strains ◽  
Culture Independent ◽  
The One

High-altitude cold habitats of the Himalayas are little explored with respect to bacterial diversity. Diverse bacterial species and phylotypes obtained by culture-dependent and culture-independent approaches are reported here. Phylogenetic analysis and modulation of bacterial diversity with altitude and available organic carbon content are also described. Psychrophilic and psychrotolerant bacteria dominated the Himalayan habitats, accounting for 60% of the cultivated strains. Isolates produced one or more (up to five) hydrolytic enzymes, lipase being the one secreted by most strains (62%). Partial 16S rRNA gene sequences were obtained for 99 bacterial strains and 74 clones obtained from soil samples from the western Himalayas. Forty-five percent of cultured bacterial strains belonged to the Proteobacteria group with 39% belonging to γ-Proteobacteria. Firmicutes was the second most abundant class with 32% of the total isolates followed by Actinobacteria (16%) and Bacteroidetes (6%). Most of the strains belonged to the genus Bacillus (30%) followed by Pseudomonas (24%) and Arthrobacter (12%). In culture-independent studies, phylotypes belonging to the Proteobacteria were dominant (73%) with the majority being β-Proteobacteria (31%). The bacterial diversity exhibited an altitude gradient with a gradual decline in the number of genera with increase in altitude. The isolates exhibited close phylogenetic affinities to bacteria from other cold habitats.

scholarly journals How do Planktonic Particle Collection Methods Affect Bacterial Diversity Estimates and Community Composition in Oligo-, Meso- and Eutrophic Lakes?

2020 ◽  
Vol 11 ◽  
Author(s):  
Guijuan Xie ◽  
Xiangming Tang ◽  
Yi Gong ◽  
Keqiang Shao ◽  
Guang Gao
Keyword(s):  
Species Diversity ◽  
Pore Size ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Heterotrophic Bacteria ◽  
Lake Taihu ◽  
Rrna Gene ◽  
Eutrophic Lakes ◽  
Particle Collection ◽  
Collection Methods

Particles are hotspots of bacterial growth and nutrient recycling in aquatic ecosystems. In the study of particle-attached (PA) and/or free-living (FL) microbial assemblages, the first step is to separate particles from their surrounding water columns. Widely used collection techniques are filtration using different pore size filters, and centrifugation; however, it is unclear how the bacterial diversity, bacterial community structure (BCS) and taxonomic composition of PA assemblages are affected by different particle collection methods. To address this knowledge gap, we collected planktonic particles from eutrophic Lake Taihu, mesotrophic Lake Tianmu, and oligotrophic Lake Fuxian in China, using filtration with five pore size of filters (20, 10, 8.0, 5.0, and 3.0 μm), and centrifugation. Bacterial communities were then analyzed using Illumina MiSeq sequencing of the 16S rRNA gene. We found that PA collection method affected BCS significantly in all lakes. Centrifugation yielded the highest species diversity and lowest mean percentage of photoautotrophic Cyanobacteria in Lake Taihu, but not in the other two lakes, thus highlighting the potential compatibility of this method in the study of PA assemblage in eutrophic lakes. The high bacterial diversity and low relative percentage of Cyanobacteria was in samples retained on 5.0 μm filters in all lakes. These results suggest that collecting PA samples in lakes using filters with 5.0 μm pore size is the preferred protocol, if species diversity and heterotrophic bacteria are the top research priorities, when comparing bacterial communities in different trophic lakes at the same time. The present study offers the possibility of collecting PA samples using unified methods in oligotrophic to eutrophic lakes.

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