scholarly journals Bacterial and Archaeal Communities Variability Associated with Upwelling and Anthropogenic Pressures in the Protection Area of Arraial do Cabo (Cabo Frio region - RJ)

2015 ◽  
Vol 87 (3) ◽  
pp. 1737-1750 ◽  
Author(s):  
SERGIO A. COELHO-SOUZA ◽  
FÁBIO V. ARAÚJO ◽  
JULIANO C. CURY ◽  
HUGO E. JESUS ◽  
GILBERTO C. PEREIRA ◽  
...  
Keyword(s):  
Secondary Production ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Heterotrophic Bacteria ◽  
Coastal Region ◽  
Principal Component ◽  
Anthropogenic Pressure ◽  
Anthropogenic Pressures ◽  
Gradient Gel Electrophoresis ◽  
Protection Area ◽  
Bacterial And Archaeal Communities

ABSTRACTUpwelling systems contain a high diversity of pelagic microorganisms and their composition and activity are defined by factors like temperature and nutrient concentration. Denaturing gradient gel electrophoresis (DGGE) technique was used to verify the spatial and temporal genetic variability of Bacteria and Archaea in two stations of the Arraial do Cabo coastal region, one under upwelling pressure and another under anthropogenic pressure. In addition, biotic and abiotic variables were measured in surface and deep waters from three other stations between these stations. Six samplings were done during a year and adequately represented the degrees of upwelling and anthropogenic pressures to the system. Principal Component Analysis (PCA) showed negative correlations between the concentrations of ammonia and phosphorous with prokaryotic secondary production and the total heterotrophic bacteria. PCA also showed negative correlation between temperature and the abundance of prokaryotic cells. Bacterial and archaeal compositions were changeable as were the oceanographic conditions, and upwelling had a regional pressure while anthropogenic pressure was punctual. We suggest that the measurement of prokaryotic secondary production was associated with both Bacteria and Archaea activities, and that substrate availability and temperature determine nutrients cycling.

scholarly journals Dynamics of various viral groups infecting autotrophic plankton in Lake Geneva

2012 ◽  
Vol 3 (2) ◽  
pp. 171 ◽  
Author(s):  
Ammini Parvathi ◽  
Xu Zhong ◽  
Stéphan Jacquet
Keyword(s):  
Carbon Fixation ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Heterotrophic Bacteria ◽  
Significant Proportion ◽  
Late Summer ◽  
Lake Geneva ◽  
Tight Coupling ◽  
Virus Like Particles ◽  
Signature Genes ◽  
Gradient Gel Electrophoresis

Viral community structure and dynamics were investigated for the first time in surface waters (0–20 m) of Lake Geneva over a 5-month period between July and November 2011. Abundances of autotrophic picoplankton, heterotrophic bacteria and virus-like particles determined using flow cytometry revealed their predominance during the summer months followed by a slight decrease in fall. Two groups of viruses could be discriminated, referred to as virus-like particles (VLP) group 1 and 2. The abundance of VLP1 correlated significantly with the bacterial abundance, while that of VLP2 correlated with both chlorophyll a and picocyanobacterial abundance suggesting a tight coupling between these viral groups and bacteria or phytoplankton. The abundance of cyanomyoviruses and cyanopodoviruses varied between 7.3 × 102 ml−1 (July) to 1.2 × 104 ml−1 (November) and 5.8 × 103 ml−1 (July) to 2.2 × 104 ml−1 (September), respectively. The abundance of the picocyanobacterial hosts was in concurrence with that of the cyanophages, being higher in late summer. Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) of viral signature genes such as g20, g23, mcp, polB, psbA and psbD revealed a relatively high richness within these genes with their diversity increasing towards the summer months. The diversity of psbD was found to be particularly high and correlated with picocyanobacterial abundance suggesting that cyanophages may be directly responsible for a significant proportion of carbon fixation in Lake Geneva.

scholarly journals Microbial biodiversity in arable soils is affected by agricultural practices

2017 ◽  
Vol 31 (2) ◽  
pp. 259-271 ◽  
Author(s):  
Agnieszka Wolińska ◽  
Dorota Górniak ◽  
Urszula Zielenkiewicz ◽  
Agata Goryluk-Salmonowicz ◽  
Agnieszka Kuźniar ◽  
...  
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Agricultural Practices ◽  
Principal Component ◽  
Operational Taxonomic Unit ◽  
Simpson Index ◽  
Arable Soils ◽  
Operational Taxonomic Units ◽  
Gradient Gel Electrophoresis ◽  
Index Of Diversity ◽  
Cultivated Soils

Abstract The aim of the study was to examine the differences in microbial community structure as a result of agricultural practices. Sixteen samples of cultivated and the same number of non-cultivated soils were selected. Gel bands were identified using the GelCompar software to create the presence-absence matrix, where each band represented a bacterial operational taxonomic unit. The data were used for principal-component analysis and additionally, the Shannon- Weaver index of general diversity, Simpson index of dominance and Simpson index of diversity were calculated. Denaturing gradient gel electrophoresis profiles clearly indicated differentiation of tested samples into two clusters: cultivated and non-cultivated soils. Greater numbers of dominant operational taxonomic units (65) in non-cultivated soils were noted compared to cultivated soils (47 operational taxonomic units). This implies that there was a reduction of dominant bacterial operational taxonomic units by nearly 30% in cultivated soils. Simpson dominance index expressing the number of species weighted by their abundance amounted to 1.22 in cultivated soils, whereas a 3-fold higher value (3.38) was observed in non-cultivated soils. Land-use practices seemed to be a important factors affected on biodiversity, because more than soil type determined the clustering into groups.

scholarly journals Antifouling Coatings Influence both Abundance and Community Structure of Colonizing Biofilms: a Case Study in the Northwestern Mediterranean Sea

2014 ◽  
Vol 80 (16) ◽  
pp. 4821-4831 ◽  
Author(s):  
Mercedes Camps ◽  
Aude Barani ◽  
Gérald Gregori ◽  
Agnès Bouchez ◽  
Brigitte Le Berre ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Heterotrophic Bacteria ◽  
Content Type ◽  
Ship Hulls ◽  
Antifouling Coating ◽  
Antifouling Coatings ◽  
Gradient Gel Electrophoresis ◽  
Northwestern Mediterranean Sea ◽  
Northwestern Mediterranean

ABSTRACTWhen immersed in seawater, substrates are rapidly colonized by both micro- and macroorganisms. This process is responsible for important economic and ecological prejudices, particularly when related to ship hulls or aquaculture nets. Commercial antifouling coatings are supposed to reduce biofouling, i.e., micro- and macrofoulers. In this study, biofilms that primarily settled on seven different coatings (polyvinyl chloride [PVC], a fouling release coating [FRC], and five self-polishing copolymer coatings [SPC], including four commercial ones) were quantitatively studied, after 1 month of immersion in summer in the Toulon Bay (Northwestern Mediterranean Sea, France), by using flow cytometry (FCM), microscopy, and denaturing gradient gel electrophoresis. FCM was used after a pretreatment to separate cells from the biofilm matrix, in order to determine densities of heterotrophic bacteria, picocyanobacteria, and pico- and nanoeukaryotes on these coatings. Among diatoms, the only microphytobenthic class identified by microscopy,Licmophora,Navicula, andNitzschiawere determined to be the dominant taxa. Overall, biocide-free coatings showed higher densities than all other coatings, except for one biocidal coating, whatever the group of microorganisms. Heterotrophic bacteria always showed the highest densities, and diatoms showed the lowest, but the relative abundances of these groups varied depending on the coating. In particular, the copper-free SPC failed to prevent diatom settlement, whereas the pyrithione-free SPC exhibited high picocyanobacterial density. These results highlight the interest in FCM for antifouling coating assessment as well as specific selection among microbial communities by antifouling coatings.

scholarly journals Different Effects of Transgenic Maize and Nontransgenic Maize on Nitrogen-Transforming Archaea and Bacteria in Tropical Soils

2014 ◽  
Vol 80 (20) ◽  
pp. 6437-6445 ◽  
Author(s):  
Simone Raposo Cotta ◽  
Armando Cavalcante Franco Dias ◽  
Ivanildo Evódio Marriel ◽  
Fernando Dini Andreote ◽  
Lucy Seldin ◽  
...  
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Genetically Modified ◽  
Tropical Soils ◽  
Plant Genotype ◽  
Ammonia Oxidizing Archaea ◽  
Maize Genotype ◽  
Gradient Gel Electrophoresis ◽  
Bacterial And Archaeal Communities ◽  
The Impact ◽  
Archaeal Communities

ABSTRACTThe composition of the rhizosphere microbiome is a result of interactions between plant roots, soil, and environmental conditions. The impact of genetic variation in plant species on the composition of the root-associated microbiota remains poorly understood. This study assessed the abundances and structures of nitrogen-transforming (ammonia-oxidizing) archaea and bacteria as well as nitrogen-fixing bacteria driven by genetic modification of their maize host plants. The data show that significant changes in the abundances (revealed by quantitative PCR) of ammonia-oxidizing bacterial and archaeal communities occurred as a result of the maize host being genetically modified. In contrast, the structures of the total communities (determined by PCR-denaturing gradient gel electrophoresis) were mainly driven by factors such as soil type and season and not by plant genotype. Thus, the abundances of ammonia-oxidizing bacterial and archaeal communities but not structures of those communities were revealed to be responsive to changes in maize genotype, allowing the suggestion that community abundances should be explored as candidate bioindicators for monitoring the possible impacts of cultivation of genetically modified plants.

Comparison of nitrification performance and microbial community between submerged membrane bioreactor and conventional activated sludge system

2005 ◽  
Vol 51 (6-7) ◽  
pp. 193-200 ◽  
Author(s):  
H. Li ◽  
M. Yang ◽  
Y. Zhang ◽  
X. Liu ◽  
M. Gao ◽  
...  
Keyword(s):  
Activated Sludge ◽  
Membrane Bioreactor ◽  
Extracellular Polymeric Substances ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Heterotrophic Bacteria ◽  
Nitrite Oxidation ◽  
Submerged Membrane Bioreactor ◽  
Conventional Activated Sludge ◽  
Activated Sludge System ◽  
Gradient Gel Electrophoresis

A submerged membrane bioreactor (SMBR) and a conventional activated sludge system (CAS) were compared in parallel over a period of more than 260 days on treating synthetic ammonia-bearing inorganic wastewater without sludge purge under decreased hydraulic retention times (HRTs). Conversion of NH4+-N to NO3--N was achieved with an efficiency of over 98% at an HRT ≥ 10 h in the SMBR, while similar performance was obtained at an HRT ≥ 20 h in the CAS. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR) amplified 16S rDNA was used to monitor variations of community structures in the two systems. With the prolongation of operation, the number of DGGE bands in the SMBR gradually increased from the initial 11 bands to the final 22 bands, whereas that in the CAS varied in a range between 13 and 183 Sequence analysis indicates that Nitrosomonas sp. and Nitrospira sp. were the dominating nitrification species responsible for ammonia and nitrite oxidation, respectively. Heterotrophic bacteria like Pseudomonas sp. and Flavobacteria sp. existed in both of the systems although only inorganic wastewater was fed. Substantive accumulation of extracellular polymeric substances (EPS) in the SMBR was confirmed by scanning electron microscopy and EPS analysis.

Oral administration of kefiran exerts a bifidogenic effect on BALB/c mice intestinal microbiota

2016 ◽  
Vol 7 (2) ◽  
pp. 237-246 ◽  
Author(s):  
M.F. Hamet ◽  
M. Medrano ◽  
P.F. Pérez ◽  
A.G. Abraham
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Profile Analysis ◽  
In Situ Hybridisation ◽  
Gc Content ◽  
Principal Component ◽  
Distal Colon ◽  
Bacterial Populations ◽  
Pcr Products ◽  
Gradient Gel Electrophoresis

The activity of kefiran, the exopolysaccharide present in kefir grains, was evaluated on intestinal bacterial populations in BALB/c mice. Animals were orally administered with kefiran and Eubacteria, lactobacilli and bifidobacteria populations were monitored in faeces of mice at days 0, 2, 7, 14 and 21. Profiles obtained by Denaturing Gradient Gel Electrophoresis (DGGE) with primers for Eubacteria were compared by principal component analysis and clearly defined clusters, correlating with the time of kefiran consumption, were obtained. Furthermore, profile analysis of PCR products amplified with specific oligonucleotides for bifidobacteria showed an increment in the number of DGGE bands in the groups administered with kefiran. Fluorescent In Situ Hybridisation (FISH) with specific probes for bifidobacteria showed an increment of this population in faeces, in accordance to DGGE results. The bifidobacteria population was also studied on distal colon content after 0, 2 and 7 days of kefiran administration. Analysis of PCR products by DGGE with Eubacteria primers showed an increment in the number and intensity of bands with high GC content of mice administered with kefiran. Sequencing of DGGE bands confirmed that bifidobacteria were one of the bacterial populations modified by kefiran administration. DGGE profiles of PCR amplicons obtained by using Bifidobacterium or Lactobacillus specific primers confirmed that kefiran administration enhances bifidobacteria, however no changes were observed in Lactobacillus populations. The results of the analysis of bifidobacteria populations assessed on different sampling sites in a murine model support the use of this exopolysaccharide as a bifidogenic functional ingredient.

Allelopathic and Medicinal plant. 26. Millettia speciosa

2020 ◽  
Vol 51 (2) ◽  
pp. 125-146
Author(s):  
Nasiruddin Nasiruddin ◽  
Yu Zhangxin ◽  
Ting Zhao Chen Guangying ◽  
Minghui Ji
Keyword(s):  
Community Structure ◽  
Medicinal Plant ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Wiener Index ◽  
Pseudomonas Spp ◽  
Evenness Index ◽  
Gradient Gel Electrophoresis ◽  
Rhizosphere Pseudomonas

We grew cucumber in pots in greenhouse for 9-successive cropping cycles and analyzed the rhizosphere Pseudomonas spp. community structure and abundance by PCR-denaturing gradient gel electrophoresis and quantitative PCR. Results showed that continuous monocropping changed the cucumber rhizosphere Pseudomonas spp. community. The number of DGGE bands, Shannon-Wiener index and Evenness index decreased during the 3rd cropping and thereafter, increased up to the 7th cropping, however, however, afterwards they decreased again. The abundance of Pseudomonas spp. increased up to the 5th successive cropping and then decreased gradually. These findings indicated that the structure and abundance of Pseudomonas spp. community changed with long-term cucumber monocropping, which might be linked to soil sickness caused by its continuous monocropping.

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

The comparison of the diversity of activated sludge plants

1998 ◽  
Vol 37 (4-5) ◽  
pp. 71-78 ◽  
Author(s):  
Thomas P. Curtis ◽  
Noel G. Craine
Keyword(s):  
Cluster Analysis ◽  
Activated Sludge ◽  
Treatment Process ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Optimal Sampling ◽  
Bacterial Populations ◽  
Large Numbers ◽  
Probable Presence ◽  
Gradient Gel Electrophoresis ◽  
Sampling Regime

The explicit engineering of bacterial populations requires that we know which organisms perform which tasks. The comparison of the bacterial diversity of activated sludge plants may give important information about the functions of different bacteria. This difficult task may be made easier by the use of technologies based on 16S rRNA based techniques. In this study we have used denaturing gradient gel electrophoresis (DGGE) to determine the optimal sampling regime for comparative studies and used cluster analysis to show how plants may be quantitatively compared. We sought evidence of spatial, diurnal and intrasample variation in a number of sites. No evidence for variation was found in the plants studied and we concluded that a single sample of an activated sludge plant was sufficient for a plant to plant comparison. The cluster analysis was able to distinguish between plants, though further work is required to find the most appropriate basis for such comparisons. We found organisms from raw sewage in the mixed liquor samples, these organisms may have no functional significance in the treatment process and thus complicate plant to plant comparisons as will the probable presence of heteroduplex rDNA products. Nevertheless we believe that these drawbacks do not outweigh the advantages of being able to take and compare relatively large numbers of samples.

Sign in / Sign up

Export Citation Format

Share Document