scholarly journals Macrophyte Species Drive the Variation of Bacterioplankton Community Composition in a Shallow Freshwater Lake

2011 ◽  
Vol 78 (1) ◽  
pp. 177-184 ◽  
Author(s):  
Jin Zeng ◽  
Yuanqi Bian ◽  
Peng Xing ◽  
Qinglong L. Wu
Keyword(s):  
Community Composition ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Single Species ◽  
Freshwater Lake ◽  
Clone Libraries ◽  
Bacterioplankton Community ◽  
Macrophyte Species ◽  
Gradient Gel Electrophoresis ◽  
Microcosm Studies ◽  
Species Specific

ABSTRACTMacrophytes play an important role in structuring aquatic ecosystems. In this study, we explored whether macrophyte species are involved in determining the bacterioplankton community composition (BCC) in shallow freshwater lakes. The BCC in field areas dominated by different macrophyte species in Taihu Lake, a large, shallow freshwater lake, was investigated over a 1-year period. Subsequently, microcosm experiments were conducted to determine if single species of different types of macrophytes in an isolated environment would alter the BCC. Denaturing gradient gel electrophoresis (DGGE), followed by cloning and sequence analysis of selected samples, was employed to analyze the BCC. The DGGE results of the field investigations indicated that the BCC changed significantly from season to season and that the presence of different macrophyte species resulted in lower BCC similarities in the summer and fall. LIBSHUFF analysis of selected clone libraries from the summer demonstrated different BCCs in the water column surrounding different macrophytes. Relative to the field observations, the microcosm studies indicated that the BCC differed more pronouncedly when associated with different species of macrophytes, which was also supported by LIBSHUFF analysis of the selected clone libraries. Overall, this study suggested that macrophyte species might be an important factor in determining the composition of bacterial communities in this shallow freshwater lake and that the species-specific influence of macrophytes on BCC is variable with the season and distance.

A Study on Bacterioplankton Community Composition in a Nature Reservoir

2013 ◽  
Vol 361-363 ◽  
pp. 747-750
Author(s):  
Bing Bing Liu ◽  
Hua Yong Zhang ◽  
Song Bo Cui
Keyword(s):  
Community Composition ◽  
Clustering Analysis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Small Scale ◽  
Bacterioplankton Community ◽  
Gradient Gel Electrophoresis ◽  
Polymerase Chain ◽  
The Relationship ◽  
Total Species ◽  
Plankton Communities

The relationship between bacterioplankton community composition and environmental factors in a constructed small-scale reservoir was studied. Polymerase chain reaction (PCR) - denaturing gradient gel electrophoresis (DGGE) fingerprinting was used to detect plankton communities. Species composition of the sites was heterogeneous; 60 % of the total species were restricted to single samples and only 2 bands were found in all investigated samples. Clustering analysis illustrated a strong correlation between samples taken from same sites. Canonical correspondence analysis (CCA) results showed that bacterioplankton community composition was primarily correlated with NO3--N and CODCr. Bacterioplankton community composition could reflect the environmental conditions to some extent.

scholarly journals Development and Validation of a Nested-PCR-Denaturing Gradient Gel Electrophoresis Method for Taxonomic Characterization of Bifidobacterial Communities

2003 ◽  
Vol 69 (11) ◽  
pp. 6380-6385 ◽  
Author(s):  
R. Temmerman ◽  
L. Masco ◽  
T. Vanhoutte ◽  
G. Huys ◽  
J. Swings
Keyword(s):  
Nested Pcr ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Temporal Changes ◽  
Rrna Gene ◽  
Specific Pcr ◽  
Gradient Gel Electrophoresis ◽  
Species Specific ◽  
Taxonomic Characterization

ABSTRACT The taxonomic characterization of a bacterial community is difficult to combine with the monitoring of its temporal changes. None of the currently available identification techniques are able to visualize a “complete” community, whereas techniques designed for analyzing bacterial ecosystems generally display limited or labor-intensive identification potential. This paper describes the optimization and validation of a nested-PCR-denaturing gradient gel electrophoresis (DGGE) approach for the species-specific analysis of bifidobacterial communities from any ecosystem. The method comprises a Bifidobacterium-specific PCR step, followed by purification of the amplicons that serve as template DNA in a second PCR step that amplifies the V3 and V6-V8 regions of the 16S rRNA gene. A mix of both amplicons is analyzed on a DGGE gel, after which the band positions are compared with a previously constructed database of reference strains. The method was validated through the analysis of four artificial mixtures, mimicking the possible bifidobacterial microbiota of the human and chicken intestine, a rumen, and the environment, and of two fecal samples. Except for the species Bifidobacterium coryneforme and B. indicum, all currently known bifidobacteria originating from various ecosystems can be identified in a highly reproducible manner. Because no further cloning and sequencing of the DGGE bands is necessary, this nested-PCR-DGGE technique can be completed within a 24-h span, allowing the species-specific monitoring of temporal changes in the bifidobacterial community.

Molecular Analysis of Spoilage-Related Bacteria in Pasteurized Milk during Refrigeration by PCR and Denaturing Gradient Gel Electrophoresis

2009 ◽  
Vol 72 (3) ◽  
pp. 572-577 ◽  
Author(s):  
HONGFEI HE ◽  
JIN DONG ◽  
CHIN NYEAN LEE ◽  
YONG LI
Keyword(s):  
Shelf Life ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Plate Count ◽  
Pasteurized Milk ◽  
Milk Samples ◽  
Gradient Gel Electrophoresis ◽  
Aerobic Plate Count ◽  
Species Specific

Bacterial diversity in fluid milk products has been extensively studied in order to improve milk quality. Here, we illustrate the utility of viable counts and PCR–denaturing gradient gel electrophoresis (DGGE) for monitoring the microbial spoilage of pasteurized milk during shelf life. Five pasteurized milk samples stored at 4°C were examined at 10 and 5 days before expiration and on the expiration day. With bacterial DNA extracted directly from the samples, PCR-DGGE analysis indicated that Pseudomonas became dominant in four samples. Meanwhile, the aerobic plate count of these four samples exceeded the regulatory limit of 20,000 CFU/ml at 5 days before expiration, and the rapid psychrotrophic count markedly surpassed the aerobic plate count on the expiration day. Streptococcus and Buttiauxella spp. were detected in several samples. Sequence analysis of DGGE fragments revealed high diversity among Pseudomonas spp. in the milk samples. P. putida and P. migulae grew to high numbers during refrigerated storage. Further identification of Pseudomonas at the species level was facilitated by PCR and multiplex PCR using species-specific primers; consequently, P. fluorescens and P. fragi were observed. These results highlight an important role of Pseudomonas in the shelf life of pasteurized milk.

Genetic diversity of picoeukaryotes in eight lakes differing in trophic status

2011 ◽  
Vol 57 (2) ◽  
pp. 115-126 ◽  
Author(s):  
Biying Zhao ◽  
Meijun Chen ◽  
Ying Sun ◽  
Jiaxin Yang ◽  
Feizhou Chen
Keyword(s):  
Genetic Diversity ◽  
Community Composition ◽  
Trophic Status ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Oligotrophic Lake ◽  
Rrna Genes ◽  
Multivariate Statistical ◽  
Mesotrophic Lake ◽  
Gradient Gel Electrophoresis ◽  
Lake Xuanwu

The genetic diversity of picoeukaryotes (0.2–5.0 µm) was investigated in 8 lakes differing in trophic status in Nanjing, China. Denaturing gradient gel electrophoresis (DGGE) and cloning and sequencing of 18S rRNA genes were applied to analyze the picoeukaryotic communities. DGGE analysis showed that among the 8 lakes, the diversity of picoeukaryotes was greatest in the mesotrophic Lake Nan (24 bands) and least in the oligotrophic Lake Qian (12 bands). Cluster analysis of DGGE profiles revealed that the 8 lakes were grouped into 2 distinct clusters. Cluster 1 contained lakes Mochou, Zixia, Huashen, Nan, Pipa, and Qian, while cluster 2 contained lakes Xuanwu and Baijia. Clone libraries were constructed from the mesotrophic Lake Xuanwu and the oligotrophic Lake Zixia, and the 2 libraries were compared using the program LIBSHUFF. This analysis indicated that the picoeukaryotic community composition differed significantly between the 2 lakes (p = 0.001). A total of 25 operational taxonomic units were detected; 18 (62 clones) were related to known eukaryotic groups, while 7 (30 clones) were not affiliated with any known eukaryotic group. Alveolates and stramenopiles were the dominant groups in Lake Xuanwu, while alveolates and chlorophyta predominated in Lake Zixia. Multivariate statistical analysis indicated that the differences in the picoeukaryotic community composition of the 8 lakes might be related to trophic status and top-down regulation by metazooplankton.

scholarly journals Aquaponics using a fish farm effluent shifts bacterial communities profile in halophytes rhizosphere and endosphere

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Vanessa Oliveira ◽  
Patrícia Martins ◽  
Bruna Marques ◽  
Daniel F. R. Cleary ◽  
Ana I. Lillebø ◽  
...  
Keyword(s):  
Natural Environment ◽  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Nutrient Loads ◽  
Marine Aquaculture ◽  
Aquaculture Effluents ◽  
Specific Effects ◽  
Salicornia Ramosissima ◽  
Gradient Gel Electrophoresis ◽  
Species Specific

AbstractThe intensification of marine aquaculture raises multiple sustainability issues, namely the handling of nutrient-rich effluents that can adversely impact ecosystems. As integrated multi-trophic aquaculture (IMTA) gains momentum, the use of halophyte plants to phytoremediate aquaculture effluents has received growing attention, particularly in aquaponics. It is, therefore, important to obtain a more in-depth knowledge of the microbial communities present in the root systems of these plants, both in their natural environment (sediment) and in aquaponics, in order to understand their nutrient removal potential. The present study used denaturing gradient gel electrophoresis (DGGE) and barcoded pyrosequencing to assess the bacterial community present in the endosphere and rhizosphere of three halophyte plants: Halimione portulacoides, Salicornia ramosissima and Sarcocornia perennis. Species-specific effects were recorded in the profile and diversity of the bacterial communities present in halophyte roots, with significant differences also recorded for the same halophyte species grown in contrasting environments (sediment vs. aquaponics). In aquaponics the most abundant groups belonged to the orders Rhodocyclales, Campylobacterales, Rhodobacterales and Desulfobacterales, while in the natural environment (sediment) the most abundant groups belonged to the orders Rhizobiales, Sphingomonadales and Alteromonadales. An overall enrichment in bacterial taxa involved in nutrient cycling was recorded in the roots of halophytes grown in aquaponics (such as Denitromonas, Mesorhizobium, Colwellia, Dokdonella and Arcobacter), thereby highlighting their potential to reduce the nutrient loads from aquaculture effluents.

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