scholarly journals Actinobacteria Structure in Autogenic, Hydrogenic and Lithogenic Cultivated and Non-Cultivated Soils: A Culture-Independent Approach

Agronomy ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 598 ◽  
Author(s):  
Agnieszka Wolińska ◽  
Dorota Górniak ◽  
Urszula Zielenkiewicz ◽  
Agnieszka Kuźniar ◽  
Dariusz Izak ◽  
...  
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Precise Determination ◽  
Total Carbon ◽  
Soil Genesis ◽  
Factors Affecting ◽  
Two Factors ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis ◽  
Next Generation Sequencing Ngs

The aim of the study was to determine the Actinobacteria structure in cultivated (C) versus non-cultivated (NC) soils divided into three groups (autogenic, hydrogenic, lithogenic) with consideration its formation process in order to assess the Actinobacteria sensitivity to agricultural soil use and soil genesis and to identify factors affecting their abundance. Sixteen C soil samples and sixteen NC samples serving as controls were taken for the study. Next generation sequencing (NGS) of the 16S rRNA metagenomic amplicons (Ion Torrent™ technology) and Denaturing Gradient Gel Electrophoresis (DGGE) were applied for precise determination of biodiversity. Generally, greater abundance of Actinobacteria in the NC soils relative to the C soils was found. Moreover, it was indicated that the actinobacterial diversity depended on both the soil genesis and the land use; however, this effect directly depended on the particular family and genera. Two factors: redox potential (Eh) and total carbon (TC) seemed to had a significant effect on the diversity of Actinobacteria. More precisely, Actinobacteria from the NC soils displayed a greater affinity for each other and were clearly influenced by Eh, whilst those from the C soils were mostly influenced by TC.

scholarly journals Polyphasic Study of the Spatial Distribution of Microorganisms in Mexican Pozol, a Fermented Maize Dough, Demonstrates the Need for Cultivation-Independent Methods To Investigate Traditional Fermentations

1999 ◽  
Vol 65 (12) ◽  
pp. 5464-5473 ◽  
Author(s):  
Frédéric Ampe ◽  
Nabil ben Omar ◽  
Claire Moizan ◽  
Carmen Wacher ◽  
Jean-Pierre Guyot
Keyword(s):  
Lactic Acid ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Fermented Food ◽  
Fermented Foods ◽  
Product Analysis ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis ◽  
Traditional Fermented Foods

ABSTRACT The distribution of microorganisms in pozol balls, a fermented maize dough, was investigated by a polyphasic approach in which we used both culture-dependent and culture-independent methods, including microbial enumeration, fermentation product analysis, quantification of microbial taxa with 16S rRNA-targeted oligonucleotide probes, determination of microbial fingerprints by denaturing gradient gel electrophoresis (DGGE), and 16S ribosomal DNA gene sequencing. Our results demonstrate that DGGE fingerprinting and rRNA quantification should allow workers to precisely and rapidly characterize the microbial assemblage in a spontaneous lactic acid fermented food. Lactic acid bacteria (LAB) accounted for 90 to 97% of the total active microflora; no streptococci were isolated, although members of the genus Streptococcus accounted for 25 to 50% of the microflora. Lactobacillus plantarum and Lactobacillus fermentum, together with members of the generaLeuconostoc and Weissella, were the other dominant organisms. The overall activity was more important at the periphery of a ball, where eucaryotes, enterobacteria, and bacterial exopolysacharide producers developed. Our results also showed that the metabolism of heterofermentative LAB was influenced in situ by the distribution of the LAB in the pozol ball, whereas homolactic fermentation was controlled primarily by sugar limitation. We propose that starch is first degraded by amylases from LAB and that the resulting sugars, together with the lactate produced, allow a secondary flora to develop in the presence of oxygen. Our results strongly suggest that cultivation-independent methods should be used to study traditional fermented foods.

MICROBIAL COMMUNITY DURING BIOREMEDIATION EXPERIMENTAL ON OIL SPILL IN COASTAL OF PARI ISLAND

2011 ◽  
Vol 3 (1) ◽  
Author(s):  
Lies Indah Sutiknowati
Keyword(s):  
Oil Spill ◽  
Deoxyribonucleic Acid ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Gas Chromatography Mass Spectrometry ◽  
Oil Degradation ◽  
Sequence Determination ◽  
Blast Search ◽  
Degrading Bacteria ◽  
Gradient Gel Electrophoresis

There is an information how to identify hydrocarbon degrading bacteria for bioremediation of marine oil spill. We have Bioremediation treatment for degradation of oil spill on Pari island and need two kind of experiment there are tanks experiment (sampling 0 to 90 days) and semi enclosed system (sampling 0 to 150 days). Biostimulation with nutrients (N and P) was done to analyze biodegradation of hydrocarbon compounds. Experiment design using fertilizer Super IB and Linstar will stimulate bacteria can degrade oil, n-alkane, and alkane as poly aromatic hydrocarbon. The bacteria communities were monitored and analyzed by Denaturing Gradient Gel Electrophoresis (DGGE) and Clone Library; oil chemistry was analyzed by Gas Chromatography Mass Spectrometry (GCMS). DNA (deoxyribonucleic acid) was extracted from colonies of bacteria and sequence determination of the 16S rDNA was amplified by primers U515f and U1492r. Strains had been sequence and had similarity about 90-99% to their closest taxa by homology Blast search and few of them suspected as new species. The results showed that fertilizers gave a significant effect on alkane, PAH and oil degradation in tanks experiment but not in the field test. Dominant of the specific bacteria on this experiment were Alcanivorax, Marinobacter and Prosthecochloris. Keywords: Bioremediation, Biostimulation, DGGE, PAH, Pari Island

scholarly journals MICROBIAL COMMUNITY DURING BIOREMEDIATION EXPERIMENTAL ON OIL SPILL IN COASTAL OF PARI ISLAND

2011 ◽  
Vol 3 (1) ◽  
Author(s):  
Lies Indah Sutiknowati
Keyword(s):  
Oil Spill ◽  
Deoxyribonucleic Acid ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Gas Chromatography Mass Spectrometry ◽  
Oil Degradation ◽  
Sequence Determination ◽  
Blast Search ◽  
Degrading Bacteria ◽  
Gradient Gel Electrophoresis

There is an information how to identify hydrocarbon degrading bacteria for bioremediation of marine oil spill. We have Bioremediation treatment for degradation of oil spill on Pari island and need two kind of experiment there are tanks experiment (sampling 0 to 90 days) and semi enclosed system (sampling 0 to 150 days). Biostimulation with nutrients (N and P) was done to analyze biodegradation of hydrocarbon compounds. Experiment design using fertilizer Super IB and Linstar will stimulate bacteria can degrade oil, n-alkane, and alkane as poly aromatic hydrocarbon. The bacteria communities were monitored and analyzed by Denaturing Gradient Gel Electrophoresis (DGGE) and Clone Library; oil chemistry was analyzed by Gas Chromatography Mass Spectrometry (GCMS). DNA (deoxyribonucleic acid) was extracted from colonies of bacteria and sequence determination of the 16S rDNA was amplified by primers U515f and U1492r. Strains had been sequence and had similarity about 90-99% to their closest taxa by homology Blast search and few of them suspected as new species. The results showed that fertilizers gave a significant effect on alkane, PAH and oil degradation in tanks experiment but not in the field test. Dominant of the specific bacteria on this experiment were Alcanivorax, Marinobacter and Prosthecochloris. Keywords: Bioremediation, Biostimulation, DGGE, PAH, Pari Island

scholarly journals Determination of the microbial flora in traditional İzmir Tulum cheeses by Denaturing Gradient Gel Electrophoresis

2018 ◽  
Vol 55 (3) ◽  
pp. 956-963 ◽  
Author(s):  
Burcin Karabey ◽  
Didem Eroglu ◽  
Caner Vural ◽  
Guven Ozdemir ◽  
Oktay Yerlikaya ◽  
...  
Keyword(s):  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Microbial Flora ◽  
Gradient Gel Electrophoresis

Factors affecting microbial fuel cell acclimation and operation in temperate climates

2013 ◽  
Vol 67 (11) ◽  
pp. 2568-2575 ◽  
Author(s):  
I. S. Michie ◽  
J. R. Kim ◽  
R. M. Dinsdale ◽  
A. J. Guwy ◽  
G. C. Premier
Keyword(s):  
Fuel Cell ◽  
Microbial Fuel Cell ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Scale Up ◽  
Reactor Performance ◽  
Trophic Conditions ◽  
Factors Affecting ◽  
Gradient Gel Electrophoresis ◽  
The Stability ◽  
Substrate Types

For the successful scale-up of microbial fuel cell (MFC) systems, enrichment strategies are required that not only maximise reactor performance but also allow anodic biofilms to be robust to environmental change. Cluster analysis of Denaturing Gradient Gel Electrophoresis community fingerprints showed that anodic biofilms were enriched according to substrate type and temperature. Acetate produced the highest power density of 7.2 W m−3 and butyrate the lowest at 0.29 W m−3, but it was also found that the trophic conditions used to acclimate the electrogenic biofilms also determined the MFC response to different substrate types, with both acetate and butyrate substrates recording power densities of 1.07 and 1.0 W m−3 respectively in a sucrose enriched reactor. When temperature perturbations were introduced to investigate the stability of the different substrate acclimated electrogenic biofilms, the 20 °C acclimated acetate reactor was unaffected by 10 °C operation but all reactors acclimated at 35 °C were adversely affected. When the operating temperature was raised back to 35 °C both the acetate and butyrate reactors recovered electrogenic activity but the sucrose reactor did not. It is thought that this was due to the more complex syntropic interactions that are required to occur when metabolising more complex substrate types.

scholarly journals Characterization of Protistan Assemblages in the Ross Sea, Antarctica, by Denaturing Gradient Gel Electrophoresis

2004 ◽  
Vol 70 (4) ◽  
pp. 2028-2037 ◽  
Author(s):  
Rebecca J. Gast ◽  
Mark R. Dennett ◽  
David A. Caron
Keyword(s):  
Species Composition ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Ross Sea ◽  
Morphological Characterization ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis ◽  
Ice Floes ◽  
Protistan Species

ABSTRACT The diversity of protistan assemblages has traditionally been studied using microscopy and morphological characterization, but these methods are often inadequate for ecological studies of these communities because most small protists inherently lack adequate taxonomic characters to facilitate their identification at the species level and many protistan species also do not preserve well. We have therefore used a culture-independent approach (denaturing gradient gel electrophoresis [DGGE]) to obtain an assessment of the genetic composition and distribution of protists within different microhabitats (seawater, meltwater or slush on sea-ice floes, and ice) of the Ross Sea, Antarctica. Samples of the same type (e.g., water) shared more of the same bands than samples of different types (e.g., ice versus water), despite being collected from different sites. These findings imply that samples from the same environment have a similar protistan species composition and that the type of microenvironment significantly influences the protistan species composition of these Antarctic assemblages. It should be noted that a large number of bands among the samples within each microhabitat were distinct, indicating the potential presence of significant genetic diversity within each microenvironment. Sequence analysis of selected DGGE bands revealed sequences that represent diatoms, dinoflagellates, ciliates, flagellates, and several unidentified eukaryotes.

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