DNA extraction procedure affects organic-aggregate-attached bacterial community profiles from a shallow eutrophic lake

2009 ◽  
Vol 55 (6) ◽  
pp. 776-782 ◽  
Author(s):  
Xiangming Tang ◽  
Guang Gao ◽  
Liping Zhu ◽  
Jianying Chao ◽  
Boqiang Qin
Keyword(s):  
Bacterial Community ◽  
Dna Extraction ◽  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Lake Taihu ◽  
Bacterial Community Composition ◽  
Extraction Procedure ◽  
Eutrophic Lake ◽  
Hexadecyltrimethylammonium Bromide ◽  
Shallow Eutrophic Lake

Organic aggregates (OA) in aquatic ecosystems harbour diverse microbial communities. The colonization and growth of OA-attached bacteria are important processes in the degradation and transformation of the particles. The development of efficient and comparative DNA extraction methods is one of the most critical steps in the study of the composition and diversity of OA-attached bacterial communities. To evaluate whether different DNA extraction procedures affect the measurement of bacterial community composition, we compared four in situ lysis procedures using OA from three locations in a shallow eutrophic lake (Lake Taihu, China). The extracted DNA was analyzed using denaturing gradient gel electrophoresis profiles. We found that the choice of DNA extraction protocol had a significant influence on the fingerprints of the OA-attached bacterial community. This was shown not only in the number of bands but also in their relative representation of certain DNA bands. Using the bead-beating DNA extraction method in the presence of hexadecyltrimethylammonium bromide, we found that crude microbial DNA could be extracted efficiently from different OA types. This protocol is reproducible and gives very pure DNA of relatively high molecular mass. More importantly, the protocol provided more representative and informative data on the diversity of OA-attached bacterial communities.

Spatial distribution of bacterial communities in sediment of a eutrophic lake revealed by denaturing gradient gel electrophoresis and multivariate analysis

2008 ◽  
Vol 54 (12) ◽  
pp. 1053-1063 ◽  
Author(s):  
Jin Zeng ◽  
Liu-Yan Yang ◽  
Yi Liang ◽  
Jia-Yun Li ◽  
Lin Xiao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Community Composition ◽  
Eutrophic Lake ◽  
Freshwater Ecosystems ◽  
Scaling Analysis ◽  
Gradient Gel Electrophoresis ◽  
Lake Xuanwu

Bacterial community structure and the effects of several environmental factors on the microbial community distribution were investigated in the sediment of the eutrophic Lake Xuanwu. Profiles of bacterial communities were generated using denaturing gradient gel electrophoresis (DGGE), and the results were interpreted with multivariate statistical analysis. Five major variables in sediment were examined in a principal component analysis, which indicates notable differences of physicochemical parameters among different sites of the lake. To assess changes in the genetic diversity of bacterial communities of different sampling sites, DGGE band patterns were analyzed by multidimensional scaling analysis, which indicated that sampling sites having similar environmental characteristics also have the similar microbial communities. Canonical correspondence analysis demonstrated that pH and redox potential had significant effects on the bacterial community composition in the sediments. Analysis of DNA sequences revealed that the dominant bacterial groups in Lake Xuanwu belonged to Proteobacteria , Actinobacteria , Verrucomicrobia , and Nitrospirae , which are commonly isolated from freshwater ecosystems.

Comparing sediment bacterial communities in the macrophyte-dominated and algae-dominated areas of eutrophic Lake Taihu, China

2011 ◽  
Vol 57 (4) ◽  
pp. 263-272 ◽  
Author(s):  
Keqiang Shao ◽  
Guang Gao ◽  
Boqiang Qin ◽  
Xiangming Tang ◽  
Yongping Wang ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Bacterial Community ◽  
Dna Sequences ◽  
Lake Taihu ◽  
Bacterial Community Composition ◽  
Eutrophic Lake ◽  
Banding Patterns ◽  
Factors Affecting ◽  
Specific Variation ◽  
Area Variation

Bacterial community structure and the effects of several environmental factors on bacterial community distribution were investigated in the sediment of the macrophyte-dominated and algae-dominated areas in a large, shallow, eutrophic freshwater lake (Lake Taihu, China). Surface sediment samples were collected at 6 sampling sites (3 sites from each of the 2 areas) on 15 February and 15 August 2009. Based on cluster analysis of the DGGE banding patterns, there were significant seasonal variations in the structure of the sediment bacterial community in the macrophyte- and algae-dominated areas, and site-specific variation within an area and between 2 areas. However, there were no significant between-area variations due to the large within-area variation. Analysis of DNA sequences showed that there were differences in the species composition of the sediment bacteria between the macrophyte- and algae-dominated area clone libraries. In the macrophyte-dominated area library, the bacterial community was dominated by Deltaproteobacteria, Verrucomicrobia, Acidobacteria, Bacteroidetes, Gammaproteobacteria, and Betaproteobacteria. OP10 was found in the library of this area but not in the algae-dominated area library. The algae-dominated area library was dominated by Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Acidobacteria. Cyanobacteria, Alphaproteobacteria, and Planctomycetes were found in this area library but not in the macrophyte-dominated area library. Canonical correspondence analysis demonstrated that total phosphorus and water temperature were the dominant environmental factors affecting bacterial community composition in the sediment.

Effects of benthic macrofauna bioturbation on the bacterial community composition in lake sediments

2014 ◽  
Vol 60 (8) ◽  
pp. 517-524 ◽  
Author(s):  
Jin Zeng ◽  
Da-Yong Zhao ◽  
Peng Liu ◽  
Zhong-Bo Yu ◽  
Rui Huang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Lake Taihu ◽  
Bacterial Community Composition ◽  
Chemical Properties ◽  
Eutrophic Lake ◽  
Benthic Macrofauna ◽  
Chironomidae Larvae ◽  
Culture Independent ◽  
Tubificid Worms

Benthic macrofauna are considered to be an important part of the lacustrine ecosystem, and bioturbation may greatly affect the biogeochemical processes and microbial activities in sediments. In the present study, the bacterial community composition in sediments inhabited by 3 different types of benthic macrofauna (Corbicula fluminea, Chironomidae larvae, and tubificid worms) in the shallow and eutrophic Lake Taihu was studied to investigate the different effects of bioturbation on the composition of these communities. Microcosms were constructed, and culture-independent methods, including terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis, were performed to evaluate the bacterial communities. Analysis of similarities (ANOSIM) and multidimensional scaling (MDS) analysis of T-RFLP patterns demonstrated that differences in the bacterial community composition between the control and the macrofauna-inhabited sediments were not as great as expected, although the chemical properties of the sediments changed remarkably. Nevertheless, the dominant bacterial group in each type of macrofauna-inhabited sediment was different. Acidobacteria, Betaproteobacteria, and Deltaproteobacteria were the dominant bacterial groups in sediments inhabited by C. fluminea, tubificid worms, and Chironomidae larvae, respectively. The data obtained in this study are helpful for understanding the effects of bioturbation in a shallow, eutrophic lake.

scholarly journals Impact of enzymatic digestion on bacterial community composition in CF airway samples

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3362 ◽  
Author(s):  
Kayla M. Williamson ◽  
Brandie D. Wagner ◽  
Charles E. Robertson ◽  
Emily J. Johnson ◽  
Edith T. Zemanick ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Dna Extraction ◽  
Community Composition ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Diversity Index ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Enzymatic Digestion ◽  
Rrna Gene

BackgroundPrevious studies have demonstrated the importance of DNA extraction methods for molecular detection ofStaphylococcus,an important bacterial group in cystic fibrosis (CF). We sought to evaluate the effect of enzymatic digestion (EnzD) prior to DNA extraction on bacterial communities identified in sputum and oropharyngeal swab (OP) samples from patients with CF.MethodsDNA from 81 samples (39 sputum and 42 OP) collected from 63 patients with CF was extracted in duplicate with and without EnzD. Bacterial communities were determined by rRNA gene sequencing, and measures of alpha and beta diversity were calculated. Principal Coordinate Analysis (PCoA) was used to assess differences at the community level and Wilcoxon Signed Rank tests were used to compare relative abundance (RA) of individual genera for paired samples with and without EnzD.ResultsShannon Diversity Index (alpha-diversity) decreased in sputum and OP samples with the use of EnzD. Larger shifts in community composition were observed for OP samples (beta-diversity, measured by Morisita-Horn), whereas less change in communities was observed for sputum samples. The use of EnzD with OP swabs resulted in significant increase in RA for the generaGemella(p < 0.01),Streptococcus(p < 0.01), andRothia(p < 0.01).Staphylococcus(p < 0.01) was the only genus with a significant increase in RA from sputum, whereas the following genera decreased in RA with EnzD:Veillonella(p < 0.01),Granulicatella(p < 0.01),Prevotella(p < 0.01), andGemella(p = 0.02). In OP samples, higher RA of Gram-positive taxa was associated with larger changes in microbial community composition.DiscussionWe show that the application of EnzD to CF airway samples, particularly OP swabs, results in differences in microbial communities detected by sequencing. Use of EnzD can result in large changes in bacterial community composition, and is particularly useful for detection ofStaphylococcusin CF OP samples. The enhanced identification ofStaphylococcus aureusis a strong indication to utilize EnzD in studies that use OP swabs to monitor CF airway communities.

Mucus composition and bacterial communities associated with the tissue and skeleton of three scleractinian corals maintained under culture conditions

2010 ◽  
Vol 91 (3) ◽  
pp. 649-657 ◽  
Author(s):  
Pascale Tremblay ◽  
Markus G. Weinbauer ◽  
Cécile Rottier ◽  
Yann Guérardel ◽  
Christian Nozais ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Coral Species ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Close Association ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Coral Tissue ◽  
Species Specific

Corals live in close association with bacterial communities, but the nature of the relationship is still poorly understood. In this study, three scleractinian coral species,Galaxea fascicularis, Pavona cactusandTurbinaria reniformiswere incubated under different laboratory conditions, and the composition of the bacterial community associated with their tissue or skeleton was compared between species or between species and seawater using denaturing gradient gel electrophoresis (DGGE). The amount of dissolved organic carbon (DOC) excreted and the mucus glycoconjugate composition were also determined for each species. The aim of the study was to assess if the bacterial community composition was species-specific or linked either to the seawater composition, or to the quality and quantity of carbon released by each coral. Results obtained showed that DOC release was significantly different (P< 0.0001) for the three species, with the highest excretion rate forG. fascicularis. Also, the mucus ofG. fascicularisandP. cactusmainly contained galactose and glucose whereas the mucus ofT. reniformiscontained more glucose and xylose. Cluster analyses of microbial community composition showed that the bacterial community was species-specific in the coral tissue but not in the skeleton, in all conditions. It remained specific when corals were incubated in the same or in different aquaria, and under different seawater renewal rates. Since DOC release rates and bacterial composition were both different according to the coral species considered, a link might be suggested between the two parameters. Sequencing of DGGE bands indicated that some bacterial phylotypes were consistently retrieved in all samples of a given species.

scholarly journals Bacterial Community Composition in Produced Water of Diyarbakır Oil Fields in Turkey : Bacterial communities in produced waters of south-eastern Turkey reported in detail for the first time

2020 ◽  
Vol 64 (4) ◽  
pp. 452-466
Author(s):  
Tuğçe Tüccar ◽  
Esra Ilhan-Sungur ◽  
Gerard Muyzer
Keyword(s):  
Bacterial Community ◽  
Water Samples ◽  
Bacterial Communities ◽  
Produced Water ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Community Composition ◽  
Oil Fields ◽  
Rrna Gene ◽  
Gradient Gel Electrophoresis ◽  
First Time

Oil fields harbour a wide variety of microorganisms with different metabolic capabilities. To examine the microbial ecology of petroleum reservoirs, a molecular-based approach was used to assess the composition of bacterial communities in produced water of Diyarbakır oil fields in Turkey. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rRNA gene fragments was performed to characterise the bacterial community structure of produced water samples and to identify predominant community members after sequencing of separated DGGE bands. The majority of bacterial sequences retrieved from DGGE analysis of produced water samples belonged to unclassified bacteria (50%). Among the classified bacteria, Proteobacteria (29.2%), Firmicutes (8.3%), Bacteroidetes (8.3%) and Actinobacteria (4.2%) groups were identified. Pseudomonas was the dominant genus detected in the produced water samples. The results of this research provide, for the first time, insight into the complexity of microbial communities in the Diyarbakır oil reservoirs and their dominant constituents.

Sign in / Sign up

Export Citation Format

Share Document