scholarly journals Effect of Model Sorptive Phases on Phenanthrene Biodegradation: Molecular Analysis of Enrichments and Isolates Suggests Selection Based on Bioavailability

2000 ◽  
Vol 66 (7) ◽  
pp. 2703-2710 ◽  
Author(s):  
M. Friedrich ◽  
R. J. Grosser ◽  
E. A. Kern ◽  
W. P. Inskeep ◽  
D. M. Ward
Keyword(s):  
Natural Organic Matter ◽  
Contaminated Soils ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Solid Phase ◽  
Cation Exchange Resin ◽  
16S Rrna Sequence ◽  
Enrichment Cultures ◽  
Gradient Gel Electrophoresis ◽  
Weak Cation Exchange ◽  
And Control

ABSTRACT Reduced bioavailability of nonpolar contaminants due to sorption to natural organic matter is an important factor controlling biodegradation of pollutants in the environment. We established enrichment cultures in which solid organic phases were used to reduce phenanthrene bioavailability to different degrees (R. J. Grosser, M. Friedrich, D. M. Ward, and W. P. Inskeep, Appl. Environ. Microbiol. 66:2695–2702, 2000). Bacteria enriched and isolated from contaminated soils under these conditions were analyzed by denaturing gradient gel electrophoresis (DGGE) and sequencing of PCR-amplified 16S ribosomal DNA segments. Compared to DGGE patterns obtained with enrichment cultures containing sand or no sorptive solid phase, different DGGE patterns were obtained with enrichment cultures containing phenanthrene sorbed to beads of Amberlite IRC-50 (AMB), a weak cation-exchange resin, and especially Biobead SM7 (SM7), a polyacrylic resin that sorbed phenanthrene more strongly. SM7 enrichments selected for mycobacterial phenanthrene mineralizers, whereas AMB enrichments selected for a Burkholderia sp. that degrades phenanthrene. Identical mycobacterial andBurkholderia 16S rRNA sequence segments were found in SM7 and AMB enrichment cultures inoculated with contaminated soil from two geographically distant sites. Other closely relatedBurkholderia sp. populations, some of which utilized phenanthrene, were detected in sand and control enrichment cultures. Our results are consistent with the hypothesis that different phenanthrene-utilizing bacteria inhabiting the same soils may be adapted to different phenanthrene bioavailabilities.

scholarly journals Effect of Model Sorptive Phases on Phenanthrene Biodegradation: Different Enrichment Conditions Influence Bioavailability and Selection of Phenanthrene-Degrading Isolates

2000 ◽  
Vol 66 (7) ◽  
pp. 2695-2702 ◽  
Author(s):  
Robert J. Grosser ◽  
Michael Friedrich ◽  
David M. Ward ◽  
William P. Inskeep
Keyword(s):  
Organic Contaminants ◽  
Contaminated Soils ◽  
Solid Phase ◽  
Enrichment Culture ◽  
Cation Exchange Resin ◽  
Culture Conditions ◽  
Phenanthrene Degradation ◽  
Initial Inoculum ◽  
Enrichment Cultures ◽  
Degradation Rates

ABSTRACT The sorption of organic contaminants by natural organic matter (NOM) often limits substrate bioavailability and is an important factor affecting microbial degradation rates in soils and sediments. We hypothesized that reduced substrate bioavailability might influence which microbial assemblages are responsible for contaminant degradation under enrichment culture conditions. Our primary goal was to characterize enrichments in which different model organic solid phases were used to establish a range of phenanthrene bioavailabilities for soil microorganisms. Phenanthrene sorption coefficients (expressed as log KD values) ranged from 3.0 liters kg−1 for Amberlite carboxylic acid cation-exchange resin (AMB) to 3.5 liters kg−1 for Biobeads polyacrylic resin (SM7) and 4.2 liters kg−1 for Biobeads divinyl benzene resin (SM2). Enrichment cultures were established for control (no sorptive phase), sand, AMB, SM7, and SM2 treatments by using two contaminated soils (from Dover, Ohio, and Libby, Mont.) as the initial inocula. The effects of sorption by model phases on the degradation of phenanthrene were evaluated for numerous transfers in order to obtain stable microbial assemblages representative of sorptive and nonsorptive enrichment cultures and to eliminate the effects of the NOM present in the initial inoculum. Phenanthrene degradation rates were similar for each soil inoculum and ranged from 4 to 5 μmol day−1 for control and sand treatments to approximately 0.4 μmol day−1 in the presence of the SM7 sorptive phase. The rates of phenanthrene degradation in the highly sorptive SM2 enrichment culture were insignificant; consequently, stable microbial populations could not be obtained. Bacterial isolates obtained from serial dilutions of enrichment culture samples exhibited significant differences in rates of phenanthrene degradation performed in the presence of SM7, suggesting that enrichments performed in the presence of a sorptive phase selected for different microbial assemblages than control treatments containing solid phase phenanthrene.

scholarly journals Simultaneous Cellulose Degradation and Electricity Production by Enterobacter cloacae in a Microbial Fuel Cell

2009 ◽  
Vol 75 (11) ◽  
pp. 3673-3678 ◽  
Author(s):  
Farzaneh Rezaei ◽  
Defeng Xing ◽  
Rachel Wagner ◽  
John M. Regan ◽  
Tom L. Richard ◽  
...  
Keyword(s):  
16S Rrna ◽  
Microbial Fuel Cells ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Cellulose Degradation ◽  
Enterobacter Cloacae ◽  
Community Analysis ◽  
Electricity Production ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Gradient Gel Electrophoresis

ABSTRACT Electricity can be directly generated by bacteria in microbial fuel cells (MFCs) from many different biodegradable substrates. When cellulose is used as the substrate, electricity generation requires a microbial community with both cellulolytic and exoelectrogenic activities. Cellulose degradation with electricity production by a pure culture has not been previously demonstrated without addition of an exogenous mediator. Using a specially designed U-tube MFC, we enriched a consortium of exoelectrogenic bacteria capable of using cellulose as the sole electron donor. After 19 dilution-to-extinction serial transfers of the consortium, 16S rRNA gene-based community analysis using denaturing gradient gel electrophoresis and band sequencing revealed that the dominant bacterium was Enterobacter cloacae. An isolate designated E. cloacae FR from the enrichment was found to be 100% identical to E. cloacae ATCC 13047T based on a partial 16S rRNA sequence. In polarization tests using the U-tube MFC and cellulose as a substrate, strain FR produced 4.9 ± 0.01 mW/m2, compared to 5.4 ± 0.3 mW/m2 for strain ATCC 13047T. These results demonstrate for the first time that it is possible to generate electricity from cellulose using a single bacterial strain without exogenous mediators.

Methanotrophic diversity in high arctic wetlands on the islands of Svalbard (Norway) - denaturing gradient gel electrophoresis analysis of soil DNA and enrichment cultures

2003 ◽  
Vol 49 (10) ◽  
pp. 602-612 ◽  
Author(s):  
Ingvild Wartiainen ◽  
Anne Grethe Hestnes ◽  
Mette M Svenning
Keyword(s):  
Methane Emission ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
The Arctic ◽  
Rrna Gene ◽  
Climatic Warming ◽  
Soil Dna ◽  
Enrichment Cultures ◽  
Arctic Soil ◽  
Gradient Gel Electrophoresis

The methanotrophic community in arctic soil from the islands of Svalbard, Norway (78°N) was analysed by combining group-specific PCR with PCR of the highly variable V3 region of the 16S rRNA gene and then by denaturing gradient gel electrophoresis (DGGE). Selected bands were sequenced for identification. The analyses were performed with DNA extracted directly from soil and from enrichment cultures at 10 and 20 °C. The two genera Methylobacter and Methylosinus were found in all localities studied. The DGGE band patterns were simple, and DNA fragments with single base differences were separated. The arctic tundra is a potential source of extensive methane emission due to climatic warming because of its large reservoirs of stored organic carbon. Higher temperatures due to climatic warming can cause increased methane production, and the abundance and activity of methane-oxidizing bacteria in the arctic soil may be important regulators for methane emission to the atmosphere.Key words: methanotrophic diversity, Svalbard, arctic wetland, denaturing gradient gel electrophoresis.

scholarly journals Composition of Bacterial Communities Associated with Natural and Laboratory Populations of Asobara tabida Infected with Wolbachia

2009 ◽  
Vol 75 (11) ◽  
pp. 3755-3764 ◽  
Author(s):  
Karima Zouache ◽  
Denis Voronin ◽  
Van Tran-Van ◽  
Patrick Mavingui
Keyword(s):  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Culture Methods ◽  
Asobara Tabida ◽  
The Family ◽  
Laboratory Populations ◽  
Gradient Gel Electrophoresis ◽  
Laboratory Colonies ◽  
And Control

ABSTRACT Asobara tabida wasps are fly endoparasitoids that naturally harbor three Wolbachia strains, which induce cytoplasmic incompatibility and control oogenesis. To investigate whether other bacteria play a role in wasp biology, we surveyed the bacterial communities of wild A. tabida populations originating from different regions of France and of laboratory colonies using PCR-denaturing gradient gel electrophoresis and culture methods. Proteobacteria and Firmicutes were found to be the main phyla represented in these populations. Among these were several cultured and uncultured representatives of the genera Acetobacter, Acidomonas, Bacillus, Brevibacillus, Duganella, Herbaspirillum, Pseudomonas, Staphylococcus, and Streptococcus. In addition to Wolbachia, wild individuals harbored Rickettsia, which tended to be lost when insects were reared in the laboratory. The antibiotic treatment used to generate wasp sublines singly infected with Wolbachia also affected the overall bacterial composition, with most fingerprint sequences being characteristic of the family Enterobacteriaceae. We also screened for potentially heritable endosymbionts by PCR and fluorescence in situ hybridization in stable laboratory lines, with only Wolbachia being consistently found in wasp ovaries.

scholarly journals Evaluation of Freeze-Dried Kefir Coculture as Starter in Feta-Type Cheese Production

2006 ◽  
Vol 72 (9) ◽  
pp. 6124-6135 ◽  
Author(s):  
Y. Kourkoutas ◽  
P. Kandylis ◽  
P. Panas ◽  
J. S. G. Dooley ◽  
P. Nigam ◽  
...  
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Solid Phase ◽  
Starter Culture ◽  
Gas Chromatography Mass Spectrometry ◽  
Ripening Process ◽  
Dna And Rna ◽  
Conversion Rates ◽  
Freeze Dried ◽  
Gradient Gel Electrophoresis ◽  
Species Specific

ABSTRACT The use of freeze-dried kefir coculture as a starter in the production of feta-type cheese was investigated. Maturation of the produced cheese at 4�C was monitored for up to 70 days, and the effects of the starter culture, the salting method, and the ripening process on quality characteristics were studied. The use of kefir coculture as a starter led to increased lactic acid concentrations and decreased pH values in the final product associated with significantly higher conversion rates compared to salted rennet cheese. Determination of bacterial diversity at the end of the ripening process in salted kefir and rennet cheeses by denaturing gradient gel electrophoresis technology, based on both DNA and RNA analyses, suggested a potential species-specific inhibition of members of the genera Staphylococcus and Psychrobacter by kefir coculture. The main active microbial associations in salted kefir cheese appeared to be members of the genera Pseudomonas and Lactococcus, while in salted rennet cheese, Oxalobacteraceae, Janthinobacterium, Psychrobacter, and Pseudomonas species were noted. The effect of the starter culture on the production of aroma-related compounds responsible for cheese flavor was also studied by the solid-phase microextraction-gas chromatography-mass spectrometry technique. Kefir coculture also appeared to extend the shelf life of unsalted cheese. Spoilage of kefir cheese was observed on the 9th and 20th days of preservation at 10 and 5�C, respectively, while spoilage in the corresponding rennet cheese was detected on the 7th and 16th days. Microbial counts during preservation of both types of unsalted cheese increased steadily and reached similar levels, with the exception of staphylococci, which were significantly lower in unsalted kefir cheese. All types of cheese produced with kefir as a starter were approved and accepted by the panel during the preliminary sensory evaluation compared to commercial feta-type cheese.

scholarly journals Monitoring of Microbial Metabolites and Bacterial Diversity in Beef Stored under Different Packaging Conditions

2011 ◽  
Vol 77 (20) ◽  
pp. 7372-7381 ◽  
Author(s):  
Danilo Ercolini ◽  
Ilario Ferrocino ◽  
Antonella Nasi ◽  
Maurice Ndagijimana ◽  
Pamela Vernocchi ◽  
...  
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Solid Phase ◽  
Modified Atmosphere Packaging ◽  
Storage Conditions ◽  
Proton Nuclear Magnetic Resonance ◽  
Microbial Metabolites ◽  
Content Type ◽  
H Nmr ◽  
Gradient Gel Electrophoresis ◽  
Microbial Groups

ABSTRACTBeef chops were stored at 4°C under different conditions: in air (A), modified-atmosphere packaging (MAP), vacuum packaging (V), or bacteriocin-activated antimicrobial packaging (AV). After 0 to 45 days of storage, analyses were performed to determine loads of spoilage microorganisms, microbial metabolites (by solid-phase microextraction [SPME]-gas chromatography [GC]-mass spectrometry [MS] and proton nuclear magnetic resonance [1H NMR]), and microbial diversity (by PCR–denaturing gradient gel electrophoresis [DGGE] and pyrosequencing). The microbiological shelf life of meat increased with increasing selectivity of storage conditions. Culture-independent analysis by pyrosequencing of DNA extracted directly from meat showed thatBrochothrix thermosphactadominated during the early stages of storage in A and MAP, whilePseudomonasspp. took over during further storage in A. Many different bacteria, several of which are usually associated with soil rather than meat, were identified in V and AV; however, lactic acid bacteria (LAB) dominated during the late phases of storage, andCarnobacterium divergenswas the most frequent microorganism in AV. Among the volatile metabolites, butanoic acid was associated with the growth of LAB under V and AV storage conditions, while acetoin was related to the other spoilage microbial groups and storage conditions.1H NMR analysis showed that storage in air was associated with decreases in lactate, glycogen, IMP, and ADP levels and with selective increases in levels of 3-methylindole, betaine, creatine, and other amino acids. The meat microbiota is significantly affected by storage conditions, and its changes during storage determine complex shifts in the metabolites produced, with a potential impact on meat quality.

scholarly journals The effect of absence of protozoa on rumen biohydrogenation and the fatty acid composition of lamb muscle

2007 ◽  
Vol 97 (5) ◽  
pp. 938-948 ◽  
Author(s):  
David R. Yáñez-Ruiz ◽  
Selwyn Williams ◽  
Charles J. Newbold
Keyword(s):  
Fatty Acid Composition ◽  
Fatty Acid ◽  
Acid Composition ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Vaccenic Acid ◽  
Intramuscular Fat ◽  
Bacterial Populations ◽  
Gradient Gel Electrophoresis ◽  
Cla Isomers ◽  
And Control

The effects of the absence of protozoa in the rumen of lambs on animal growth, rumen fermentation, microbial diversity and fatty acid profiles in abomasal fluid and intramuscular fat were measured in ten control and ten protozoa-free (PF) lambs. PF lambs were prepared by isolating them from ewes within the first 24 h after birth. The PF and control lambs were kept for 4 months in two different fields and received a daily supplement of 250 g concentrate. The bacterial populations visualised by denaturing gradient gel electrophoresis differed between the two groups of animals and showed a higher bacterial diversity in control lambs than in PF lambs. Abomasal contents from control lambs contained higher concentrations of 22 : 5n-3 and 22 : 6n-3 and lower concentrations of vaccenic acid (trans-11–18 : 1) and 20 : 3n-6 than PF lambs. The rest of the fatty acids, including the conjugated linoleic acid (CLA) isomers, were present at the same concentrations in abomasal contents from both experimental groups. Fatty acid composition in intramuscular fat showed differences between the groups. PF lambs had higher proportions of 18 : 0, 18 : 3,trans-10,cis-12-CLA and total SFA than control lambs. Control lambs had higher proportions ofcis-9–18 : 1,cis-9,cis-12–18 : 2, 20 : 3n-6, 22 : 6n-3 (DHA) and MUFA. In conclusion, rumen defaunation led to higher tissue levels of thetrans-10,cis-12-CLA isomer and SFA and lower PUFA:SFA ratio andn-3 PUFA in lamb muscle.

Review on Microbial Analysis Tools in POME treatment

2020 ◽  
pp. 220-240
Author(s):  
Mohamad Mokhtar Ibrahim ◽  
Zulkifly Jemaat ◽  
Abdurahman Hamid Nour
Keyword(s):  
Molecular Biology ◽  
Palm Oil ◽  
Biological Treatment ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Membrane Separation ◽  
In Situ Hybridisation ◽  
Community Analysis ◽  
Gradient Gel Electrophoresis ◽  
High Concentrations ◽  
And Control

Palm oil mill effluent (POME) is one of the major sources of water pollution in Malaysia. POME is produced in large volumes by many palm oil mills and has acidic pH and high concentrations of COD, BOD, and suspended solids, which have adverse effect to the environment. Currently, the technology to treat POME is either physical, chemical, or biological. About 80% of palm oil mills treat their POME by using biological method. Recent studies have indicated that understanding the microbial community structure is of great importance to improve and control the biological treatment performance. Currently, the most popular molecular biology tools for microorganism community analysis are fluorescence in situ hybridisation (FISH), cloning of 16S rDNA, and denaturing gradient gel electrophoresis (DGGE). This chapter aims to review the current and ongoing treatments of POME (mainly anaerobic, aerobic, physicochemical, and membrane separation) and discuss the potential of using the molecular biology techniques in POME treatment. The importance and effectiveness of the microbiology tools are also discussed. The ability to monitor microorganisms and understand their ecology is essential to effectively control the startup and operation of biological treatment system in treating POME and eventually producing effluent of acceptable quality.

Changes in Bacterial Species Composition in Enrichment Cultures with Various Dilutions of Inoculum as Monitored by Denaturing Gradient Gel Electrophoresis

1998 ◽  
Vol 64 (12) ◽  
pp. 5046-5048 ◽  
Author(s):  
Colin R. Jackson ◽  
Eric E. Roden ◽  
Perry F. Churchill
Keyword(s):  
Species Composition ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Species ◽  
Enrichment Cultures ◽  
Gradient Gel Electrophoresis ◽  
Enrichment Techniques

ABSTRACT Denaturing gradient gel electrophoresis revealed changes in the bacterial species obtained from enrichment cultures with different inoculum dilutions. This inoculum dilution enrichment approach may facilitate the detection and isolation of a greater number of bacterial species than traditional enrichment techniques.

scholarly journals Identification of and Spatio-Temporal Differences between Microbial Assemblages from Two Neighboring Sulfurous Lakes: Comparison by Microscopy and Denaturing Gradient Gel Electrophoresis

2000 ◽  
Vol 66 (2) ◽  
pp. 499-508 ◽  
Author(s):  
Emilio O. Casamayor ◽  
Hendrik Schäfer ◽  
Lluis Bañeras ◽  
Carlos Pedrós-Alió ◽  
Gerard Muyzer
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Phytoplankton Bloom ◽  
Water Source ◽  
Climatic Conditions ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Gradient Gel Electrophoresis

ABSTRACT The microbial assemblages of Lake Cisó and Lake Vilar (Banyoles, northeast Spain) were analyzed in space and time by microscopy and by performing PCR-denaturing gradient gel electrophoresis (DGGE) and sequence analysis of 16S rRNA gene fragments. Samples obtained from different water depths and at two different times of the year (in the winter during holomixis and in the early spring during a phytoplankton bloom) were analyzed. Although the lakes have the same climatic conditions and the same water source, the limnological parameters were different, as were most of the morphologically distinguishable photosynthetic bacteria enumerated by microscopy. The phylogenetic affiliations of the predominant DGGE bands were inferred by performing a comparative 16S rRNA sequence analysis. Sequences obtained from Lake Cisó samples were related to gram-positive bacteria and to members of the divisionProteobacteria. Sequences obtained from Lake Vilar samples were related to members of theCytophaga-Flavobacterium-Bacteroides phylum and to cyanobacteria. Thus, we found that like the previously reported differences between morphologically distinct inhabitants of the two lakes, there were also differences among the community members whose morphologies did not differ conspicuously. The changes in the species composition from winter to spring were also marked. The two lakes both contained sequences belonging to phototrophic green sulfur bacteria, which is consistent with microscopic observations, but these sequences were different from the sequences of cultured strains previously isolated from the lakes. Euryarchaeal sequences (i.e., methanogen- and thermoplasma-related sequences) also were present in both lakes. These euryarchaeal group sequences dominated the archaeal sequences in Lake Cisó but not in Lake Vilar. In Lake Vilar, a new planktonic population related to the crenarchaeota produced the dominant archaeal band. The phylogenetic analysis indicated that new bacterial and archaeal lineages were present and that the microbial diversity of these assemblages was greater than previously known. We evaluated the correspondence between the abundances of several morphotypes and DGGE bands by comparing microscopy and sequencing results. Our data provide evidence that the sequences obtained from the DGGE fingerprints correspond to the microorganisms that are actually present at higher concentrations in the natural system.

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