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.

Genetic Diversity of the Biofilm CoveringMontacuta ferruginosa (Mollusca, Bivalvia) as Evaluated by Denaturing Gradient Gel Electrophoresis Analysis and Cloning of PCR-Amplified Gene Fragments Coding for 16S rRNA†

1998 ◽  
Vol 64 (9) ◽  
pp. 3464-3472 ◽  
Author(s):  
David C. Gillan ◽  
Arjen G. C. L. Speksnijder ◽  
Gabriel Zwart ◽  
Chantal De Ridder
Keyword(s):  
Genetic Diversity ◽  
16S Rrna ◽  
Dna Extraction ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Gradient Gel Electrophoresis ◽  
Biofilm Bacteria ◽  
Sequence Types

The shell of the bivalve Montacuta ferruginosa, a symbiont living in the burrow of an echinoid, is covered with a rust-colored biofilm. This biofilm includes different morphotypes of bacteria that are encrusted with a mineral rich in ferric ion and phosphate. The aim of this research was to determine the genetic diversity and phylogenetic affiliation of the biofilm bacteria. Also, the possible roles of the microorganisms in the processes of mineral deposition within the biofilm, as well as their impact on the biology of the bivalve, were assessed by phenotypic inference. The genetic diversity was determined by denaturing gradient gel electrophoresis (DGGE) analysis of short (193-bp) 16S ribosomal DNA PCR products obtained with primers specific for the domain Bacteria. This analysis revealed a diverse consortium; 11 to 25 sequence types were detected depending on the method of DNA extraction used. Individual biofilms analyzed by using the same DNA extraction protocol did not produce identical DGGE profiles. However, different biofilms shared common bands, suggesting that similar bacteria can be found in different biofilms. The phylogenetic affiliations of the sequence types were determined by cloning and sequencing the 16S rRNA genes. Close relatives of the genera Pseudoalteromonas,Colwellia, and Oceanospirillum (members of the γ-Proteobacteria lineage), as well as Flexibacter maritimus (a member of theCytophaga-Flavobacter-Bacteroides lineage), were found in the biofilms. We inferred from the results that some of the biofilm bacteria could play a role in the mineral formation processes.

scholarly journals Bacterial Origin and Community Composition in the Barley Phytosphere as a Function of Habitat and Presowing Conditions

2000 ◽  
Vol 66 (10) ◽  
pp. 4372-4377 ◽  
Author(s):  
Bo Normander ◽  
Jim I. Prosser
Keyword(s):  
Community Composition ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Community Composition ◽  
Pcr Amplification ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Populations ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis

ABSTRACT An understanding of the factors influencing colonization of the rhizosphere is essential for improved establishment of biocontrol agents. The aim of this study was to determine the origin and composition of bacterial communities in the developing barley (Hordeum vulgare) phytosphere, using denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes amplified from extracted DNA. Discrete community compositions were identified in the endorhizosphere, rhizoplane, and rhizosphere soil of plants grown in an agricultural soil for up to 36 days. Cluster analysis revealed that DGGE profiles of the rhizoplane more closely resembled those in the soil than the profiles found in the root tissue or on the seed, suggesting that rhizoplane bacteria primarily originated from the surrounding soil. No change in bacterial community composition was observed in relation to plant age. Pregermination of the seeds for up to 6 days improved the survival of seed-associated bacteria on roots grown in soil, but only in the upper, nongrowing part of the rhizoplane. The potential occurrence of skewed PCR amplification was examined, and only minor cases of PCR bias for mixtures of two different DNA samples were observed, even when one of the samples contained plant DNA. The results demonstrate the application of culture-independent, molecular techniques in assessment of rhizosphere bacterial populations and the importance of the indigenous soil population in colonization of the rhizosphere.

scholarly journals Phylogenetic and Morphological Diversity of Cyanobacteria in Soil Desert Crusts from the Colorado Plateau

2001 ◽  
Vol 67 (4) ◽  
pp. 1902-1910 ◽  
Author(s):  
Ferran Garcia-Pichel ◽  
Alejandro López-Cortés ◽  
Ulrich Nübel
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Colorado Plateau ◽  
Morphological Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Filamentous Cyanobacteria ◽  
Phylogenetic Cluster ◽  
Field Samples ◽  
Gradient Gel Electrophoresis ◽  
Well Differentiated

ABSTRACT We compared the community structures of cyanobacteria in four biological desert crusts from Utah's Colorado Plateau developing on different substrata. We analyzed natural samples, cultures, and cyanobacterial filaments or colonies retrieved by micromanipulation from field samples using microscopy, denaturing gradient gel electrophoresis, and sequencing of 16S rRNA genes. While microscopic analyses apparently underestimated the biodiversity of thin filamentous cyanobacteria, molecular analyses failed to retrieve signals for otherwise conspicuous heterocystous cyanobacteria with thick sheaths. The diversity found in desert crusts was underrepresented in currently available nucleotide sequence databases, and several novel phylogenetic clusters could be identified. Morphotypes fitting the description of Microcoleus vaginatus Gomont, dominant in most samples, corresponded to a tight phylogenetic cluster of probable cosmopolitan distribution, which was well differentiated from other cyanobacteria traditionally classified within the same genus. A new, diverse phylogenetic cluster, named “Xeronema,” grouped a series of thin filamentousPhormidium-like cyanobacteria. These were also ubiquitous in our samples and probably correspond to various botanicalPhormidium and Schizothrix spp., but they are phylogenetically distant from thin filamentous cyanobacteria from other environments. Significant differences in community structure were found among soil types, indicating that soil characteristics may select for specific cyanobacteria. Gypsum crusts were most deviant from the rest, while sandy, silt, and shale crusts were relatively more similar among themselves.

scholarly journals The effect of inoculum dose on the genetic diversity detected within Helicoverpa armigera nucleopolyhedrovirus populations

2013 ◽  
Vol 94 (11) ◽  
pp. 2524-2529 ◽  
Author(s):  
Vicky Lynne Baillie ◽  
Gustav Bouwer
Keyword(s):  
Genetic Diversity ◽  
Helicoverpa Armigera ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Model System ◽  
Inoculum Dose ◽  
Significant Difference ◽  
Helicoverpa Armígera ◽  
Gradient Gel Electrophoresis ◽  
Neonate Larvae

Environmental and infection variables may affect the genetic diversity of baculovirus populations. In this study, Helicoverpa armigera nucleopolyhedrovirus (HearNPV) was used as a model system for studying the effects of a key infection variable, inoculum dose, on the genetic diversity within nucleopolyhedrovirus populations. Diversity and equitability indices were calculated from DNA polymerase-specific denaturing gradient gel electrophoresis profiles obtained from individual H. armigera neonate larvae inoculated with either an LD5 or LD95 of HearNPV. Although the genetic diversity detected in larvae treated with an LD95 was not statistically different from the diversity detected in the HearNPV inoculum samples, there was a statistically significant difference in the genetic diversity detected in the LD5-inoculated larvae compared with the genetic diversity detected in the HearNPV samples used for the inoculations. The study suggests that inoculum dose needs to be considered carefully in experiments that evaluate HearNPV genetic diversity or in studies where differences in genetic diversity may have phenotypic consequences.

Perchlorate removal using two component biodegradable carriers in particle-fixed biofilm reactor

2014 ◽  
Vol 49 (3) ◽  
pp. 234-244
Author(s):  
Fang He ◽  
Fusheng Li ◽  
Haihong Zhou ◽  
Lingling Niu ◽  
Liguo Wang
Keyword(s):  
Carbon Source ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Polymer Particle ◽  
Biofilm Reactor ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Biofilm Reactors ◽  
Gradient Gel Electrophoresis ◽  
Perchlorate Removal ◽  
Fixed Biofilm

In this research, biocompounds designed out of two polymers having different degradability was investigated for use as the sole carbon source and biofilm carrier to remove perchlorate in particle-fixed biofilm reactors. Both laboratory batch and column experiments were conducted with perchlorate contaminated groundwater. Batch experiments demonstrated clearly that ClO4– was removed from the aqueous phase readily and the degradation rate constants (k) changed in the range of 0.23–0.37 mg/L h as ClO4– concentration increased from 2 to 8 mg/L. Simultaneous perchlorate and nitrate degradation occurred in the polymer bioreactor. Effluent concentrations of perchlorate varied positively with temperature and fitted the Arrhenius equation expression as k=k20•100.0316(t–20) over the range of 13–30 °C. No perchlorate was detected in the effluent of polymer columns after 20 days’ startup. Complete perchlorate removal was observed at a hydraulic loading rate doubled to 1.8 mL/min. Images prove the concept of the pore and filament structure within the biocompounds, which provide both a heterotrophic biofilm and carbon source. Denaturing gradient gel electrophoresis analysis and partial sequencing of 16S rRNA genes indicated that formerly reported perchlorate-reducing bacteria were present in the polymer particle-fixed biofilm reactors.

scholarly journals Phylogenetic Composition of Arctic Ocean Archaeal Assemblages and Comparison with Antarctic Assemblages

2004 ◽  
Vol 70 (2) ◽  
pp. 781-789 ◽  
Author(s):  
Nasreen Bano ◽  
Shomari Ruffin ◽  
Briana Ransom ◽  
James T. Hollibaugh
Keyword(s):  
Arctic Ocean ◽  
Denaturing Gradient Gel Electrophoresis ◽  
16S Rrna Genes ◽  
The Arctic ◽  
Rrna Genes ◽  
Specific Primers ◽  
Group I ◽  
The Arctic Ocean ◽  
Gradient Gel Electrophoresis ◽  
Phylogenetic Composition

ABSTRACT Archaea assemblages from the Arctic Ocean and Antarctic waters were compared by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes amplified using the Archaea-specific primers 344f and 517r. Inspection of the DGGE fingerprints of 33 samples from the Arctic Ocean (from SCICEX submarine cruises in 1995, 1996, and 1997) and 7 Antarctic samples from Gerlache Strait and Dallman Bay revealed that the richness of Archaea assemblages was greater in samples from deep water than in those from the upper water column in both polar oceans. DGGE banding patterns suggested that most of the Archaea ribotypes were common to both the Arctic Ocean and the Antarctic Ocean. However, some of the Euryarchaeota ribotypes were unique to each system. Cluster analysis of DGGE fingerprints revealed no seasonal variation but supported depth-related differences in the composition of the Arctic Ocean Archaea assemblage. The phylogenetic composition of the Archaea assemblage was determined by cloning and then sequencing amplicons obtained from the Archaea-specific primers 21f and 958r. Sequences of 198 clones from nine samples covering three seasons and all depths grouped with marine group I Crenarchaeota (111 clones), marine group II Euryarchaeota (86 clones), and group IV Euryarchaeota (1 clone). A sequence obtained only from a DGGE band was similar to those of the marine group III Euryarchaeota.

scholarly journals Effects of Lactococcus lactis on Composition of Intestinal Microbiota: Role of Nisin

2006 ◽  
Vol 72 (1) ◽  
pp. 239-244 ◽  
Author(s):  
Nete Bernbom ◽  
Tine Rask Licht ◽  
Carl-Henrik Brogren ◽  
Birthe Jelle ◽  
Anette H. Johansen ◽  
...  
Keyword(s):  
Lactococcus Lactis ◽  
Intestinal Microbiota ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Fecal Microbiota ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Enzyme Linked Immunosorbent Assay ◽  
Gradient Gel Electrophoresis ◽  
Intact Molecule ◽  
Human Flora

ABSTRACT This study examined the ability of (i) pure nisin, (ii) nisin-producing Lactococcus lactis strain CHCC5826, and (iii) the non-nisin-producing L. lactis strain CHCH2862 to affect the composition of the intestinal microbiota of human flora-associated rats. The presence of both the nisin-producing and the non-nisin-producing L. lactis strains significantly increased the number of Bifidobacterium cells in fecal samples during the first 8 days but decreased the number of enterococci/streptococci in duodenum, ileum, cecum, and colon samples as detected by selective cultivation. No significant changes in the rat fecal microbiota were observed after dosage with nisin. Pearson cluster analysis of denaturing gradient gel electrophoresis profiles of the 16S rRNA genes present in the fecal microbial population revealed that the microbiota of animals dosed with either of the two L. lactis strains were different from that of control animals dosed with saline. However, profiles of the microbiota from animals dosed with nisin did not differ from the controls. The concentrations of nisin estimated by competitive enzyme-linked immunosorbent assay (ELISA) were approximately 10-fold higher in the small intestine and 200-fold higher in feces than the corresponding concentrations estimated by a biological assay. This indicates that nisin was degraded or inactivated in the gastrointestinal tract, since fragments of this bacteriocin are detected by ELISA while an intact molecule is needed to retain biological activity.

Changes in the structure and diversity of bacterial communities during the process of adaptation to organic wastewater

2010 ◽  
Vol 56 (4) ◽  
pp. 352-355 ◽  
Author(s):  
Junmin Li ◽  
Zexin Jin ◽  
Binbin Yu
Keyword(s):  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Similarity Index ◽  
Pcr Amplification ◽  
Genotypic Diversity ◽  
Diversity Indices ◽  
Inhibitory Effect ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Gradient Gel Electrophoresis

To explore changes in the structure and diversity of activated sludge-derived microbial communities during adaptation to gradual increases in the concentration of wastewater, RAPD–PCR and the combination of PCR amplification of 16S rRNA genes with denaturing gradient gel electrophoresis (DGGE) analysis were used. In bacterial communities exposed to 0%, 5%, 10%, 20%, or 40% wastewater, there were 27, 25, 18, 17 and 16 bands, respectively, based on DGGE data, while there were 69, 83, 97, 86, and 88 bands, respectively, based on RAPD data. The community similarity index among bacterial communities during the process of adaptation to different concentrations of wastewater was different based on DGGE and RAPD data. Based on DGGE and RAPD profiles, the Shannon–Weiner and Simpson’s diversity indices decreased sharply upon exposure to 10% wastewater, indicating that 10% wastewater might be a critical point at which the growth of bacteria could be significantly inhibited and the genotypic diversity could change. This indicated that changes in structure and diversity might have an inhibitory effect on the toxicity of organic matter and that selection and adaptation could play important roles in the changes.

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