Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Molecular biological detection and characterization of Clostridium populations in municipal landfill sites.

ABSTRACT: Primer sets specific for 16S rRNA genes were designed for four phylogenetic groups of clostridia known to contain mesophilic cellulolytic species. Specific amplification of these groups from landfill leachate DNA extracts demonstrated the widespread occurrence of clostridia from the Clostridium thermocellum and C. leptum groups. In contrast, the C. botulinum group was never detected, and the C. coccoides-C. lentocellum group was only occasionally detected. Amplification products were analyzed by temporal thermal gel electrophoresis to generate profiles of the clostridial groups and to identify dominant bands. Sequence analysis of 17 landfill clones confirmed that the primers were specific for the clostridial subgroups and that the cloned sequences had a close relationship with known cellulose-degrading clostridia. The primers have therefore been authenticated for use in the rapid identification of clostridia in anaerobic environments.

SUBMITTER: Van Dyke MI

PROVIDER: S-EPMC123838 | biostudies-literature | 2002 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Molecular biological detection and characterization of Clostridium populations in municipal landfill sites.

Van Dyke M I MI McCarthy A J AJ

Applied and environmental microbiology 20020401 4

Primer sets specific for 16S rRNA genes were designed for four phylogenetic groups of clostridia known to contain mesophilic cellulolytic species. Specific amplification of these groups from landfill leachate DNA extracts demonstrated the widespread occurrence of clostridia from the Clostridium thermocellum and C. leptum groups. In contrast, the C. botulinum group was never detected, and the C. coccoides-C. lentocellum group was only occasionally detected. Amplification products were analyzed by ...[more]

PMID: 11916731

Similar Datasets

Molecular biological detection of anaerobic gut fungi (Neocallimastigales) from landfill sites.

Project description:Oligonucleotide primers were designed for the 18S rRNA genes of members of the Neocallimastigales and used in a nested PCR protocol to amplify 787-bp fragments of DNA from landfill site samples. The specificities of the primers were confirmed by phylogenetic analysis of the environmental clone sequences, and this method can therefore now be used to investigate the ecology of the obligately anaerobic fungi. To our knowledge, this is the first demonstration of the occurrence of members of the Neocallimastigales outside the mammalian gut, and their distribution across the landfill samples examined here suggests that they are actively involved in cellulose degradation.

| S-EPMC1538735 | biostudies-literature

Functional environmental genomics of a municipal landfill soil

Project description:We investigated the toxicity of soil samples derived from a former municipal landfill site in the South of the Netherlands, where a bioremediation project is running aiming at reusing the site for recreation. Both an organic soil extract and the original soil sample was investigated using the ISO standardised Folsomia soil ecotoxicological testing and gene expression analysis. The 28 day survival/reproduction test revealed that the ecologically more relevant original soil sample was more toxic than the organic soil extract. Microarray analysis showed that the more toxic soil samples induced gene regulatory changes in twice as less genes compared to the soil extract. Consequently gene regulatory changes were highly dependent on sample type, and were to a lesser extent caused by exposure level. An important biological process shared among the two sample types was the detoxification pathway for xenobiotics (biotransformation I, II and III) suggesting a link between compound type and observed adverse effects. Finally, we were able to retrieve a selected group of genes that show highly significant dose-dependent gene expression and thus were tightly linked with adverse effects on reproduction. Expression of four cytochrome P450 genes showed highest correlation values with reproduction, and maybe promising genetic markers for soil quality. However, a more elaborate set of environmental soil samples is needed to validate the correlation between gene expression induction and adverse phenotypic effects.

2012-04-16 | GSE37154 | GEO

Identification, detection, and spatial resolution of Clostridium populations responsible for cellulose degradation in a methanogenic landfill leachate bioreactor.

Project description:An anaerobic landfill leachate bioreactor was operated with crystalline cellulose and sterile landfill leachate until a steady state was reached. Cellulose hydrolysis, acidogenesis, and methanogenesis were measured. Microorganisms attached to the cellulose surfaces were hypothesized to be the cellulose hydrolyzers. 16S rRNA gene clone libraries were prepared from this attached fraction and also from the mixed fraction (biomass associated with cellulose particles and in the planktonic phase). Both clone libraries were dominated by Firmicutes phylum sequences (100% of the attached library and 90% of the mixed library), and the majority fell into one of five lineages of the clostridia. Clone group 1 (most closely related to Clostridium stercorarium), clone group 2 (most closely related to Clostridium thermocellum), and clone group 5 (most closely related to Bacteroides cellulosolvens) comprised sequences in Clostridium group III. Clone group 3 sequences were in Clostridium group XIVa (most closely related to Clostridium sp. strain XB90). Clone group 4 sequences were affiliated with a deeply branching clostridial lineage peripherally associated with Clostridium group VI. This monophyletic group comprises a new Clostridium cluster, designated cluster VIa. Specific fluorescence in situ hybridization (FISH) probes for the five groups were designed and synthesized, and it was demonstrated in FISH experiments that bacteria targeted by the probes for clone groups 1, 2, 4, and 5 were very abundant on the surfaces of the cellulose particles and likely the key cellulolytic microorganisms in the landfill bioreactor. The FISH probe for clone group 3 targeted cells in the planktonic phase, and these organisms were hypothesized to be glucose fermenters.

| S-EPMC383074 | biostudies-literature

Quantitative determination of fluorochemicals in municipal landfill leachates.

Project description:Twenty-four fluorochemicals were quantified in landfill leachates recovered from municipal refuse using an analytical method based on solid-phase extraction, dispersive-carbon sorbent cleanup, and liquid chromatography/tandem mass spectrometry. The method was applied to six landfill leachates from four locations in the US as well as to a leachate generated by a laboratory bioreactor containing residential refuse. All seven leachates had the common characteristic that short-chain (C(4)-C(7)) carboxylates or sulfonates were greater in abundance than their respective longer-chain homologs (? C(8)). Perfluoroalkyl carboxylates were the most abundant (67 ± 4% on a nanomolar (nM) basis) fluorochemicals measured in leachates; concentrations of individual carboxylates reaching levels up to 2800 ng L(-1). Perfluoroalkyl sulfonates were the next most abundant class (22 ± 2%) on a nM basis; their abundances in each of the seven leachates derived from municipal refuse were greater for the shorter-chain homologs (C(4) and C(6)) compared to longer-chain homologs (C(8) and C(10)). Perfluorobutane sulfonate concentrations were as high as 2300 ng L(-1). Sulfonamide derivatives composed 8 ± 2.1% (nM basis) of the fluorochemicals in landfill leachates with methyl (C(4) and C(8)) and ethyl (C(8)) sulfonamide acetic acids being the most abundant. Fluorotelomer sulfonates (6:2 and 8:2) composed 2.4 ± 1.3% (nM basis) of the fluorochemicals detected and were present in all leachates.

| S-EPMC4153346 | biostudies-literature

Functional environmental genomics of a municipal landfill soil.

Project description:We investigated the toxicity of soil samples derived from a former municipal landfill site in the South of the Netherlands, where a bioremediation project is running aiming at reusing the site for recreation. Both an organic soil extract and the original soil sample was investigated using the ISO standardized Folsomia soil ecotoxicological testing and gene expression analysis. The 28 day survival/reproduction test revealed that the ecologically more relevant original soil sample was more toxic than the organic soil extract. Microarray analysis showed that the more toxic soil samples induced gene regulatory changes in twice as less genes compared to the soil extract. Consequently gene regulatory changes were highly dependent on sample type, and were to a lesser extent caused by exposure level. An important biological process shared among the two sample types was the detoxification pathway for xenobiotics (biotransformation I, II, and III) suggesting a link between compound type and observed adverse effects. Finally, we were able to retrieve a selected group of genes that show highly significant dose-dependent gene expression and thus were tightly linked with adverse effects on reproduction. Expression of four cytochrome P450 genes showed highest correlation values with reproduction, and maybe promising genetic markers for soil quality. However, a more elaborate set of environmental soil samples is needed to validate the correlation between gene expression induction and adverse phenotypic effects.

| S-EPMC3353140 | biostudies-literature

Functional environmental genomics of a municipal landfill soil

2012-04-15 | E-GEOD-37154 | biostudies-arrayexpress

Effective photochemical treatment of a municipal solid waste landfill leachate.

Project description:This work aimed at studying the photochemical treatment of a landfill leachate using ultraviolet light, hydrogen peroxide, and ferrous or ferric ions, in a batch recycle photoreactor. The effect of inorganic carbon presence, pH, initial H2O2 amount (0-9990 mg L-1) as well as Fe(II) (200-600 ppm) and Fe(III) (300-700 ppm) concentrations on the total carbon removal and color change was studied. Prior to the photochemical treatment, a pretreatment process was applied; inorganic nitrogen and inorganic carbon were removed by means of air stripping and initial pH regulation, respectively. The leachate sent subsequently for photochemical treatment was free of inorganic carbon and contained only organic carbon with concentration 1200±100 mg L-1 at pH 5.1-5.3. The most favorable concentrations of H2O2 and ferric ions for carbon removal were 6660 mg L-1 and 400 ppm, respectively. Adjusting the initial pH value in the range of 2.2-5.3 had a significant effect on the organic carbon removal. The photo-Fenton-like process was more advantageous than the photo-Fenton one for leachate treatment. By applying the most favorable operating conditions, 88.7% removal of total organic carbon, 100% removal of total inorganic carbon, 96.5% removal of total nitrogen, and 98.2% color removal were achieved.

| S-EPMC7508382 | biostudies-literature

Whole metagenome sequencing from municipal waste landfill sites

Project description:Whole metagenome sequencing from municipal waste landfill sites Metagenome

| PRJNA657696 | ENA

Molecular biological detection and quantification of novel Fibrobacter populations in freshwater lakes.

Project description:PCR and quantitative PCR (qPCR) primers targeting the 16S rRNA gene were used to detect and quantify members of the genus Fibrobacter in lake water, sediment and colonized cotton taken from two freshwater lakes. Phylogenetic analysis identified two groups of sequences; those clustered with Fibrobacter succinogenes, the type species, and a defined cluster of clones loosely associated with several Fibrobacter sequences observed previously in clone libraries from freshwater environments. 16S rRNA gene sequences recovered in the same way from soil samples and ovine feces in the surrounding land were all F. succinogenes and did not include any from this group of the "freshwater" Fibrobacteres. In all cases, nested PCR was required to detect Fibrobacter 16S rRNA genes, and qPCR analysis of reverse transcribed bacterial community RNA confirmed their very low relative abundance on colonized cotton baits in the water column (at 0, 3, 7, 11, and 13 m) and on the sediment surface (<0.02% of total bacterial rRNA). However, in Esthwaite Water sediment itself, the relative abundance of fibrobacters was 2 orders of magnitude higher (ca. 1% of total bacterial rRNA). The presence of fibrobacters, including the cellulolytic rumen species F. succinogenes, on colonized cellulose samples and in lake sediment suggests that these organisms may contribute to the primary degradation of plant and algal biomass in freshwater lake ecosystems.

| S-EPMC2725500 | biostudies-literature

Detection and molecular characterization of urinary tract HIV-1 populations.

Project description:BACKGROUND:Identification of all possible HIV reservoirs is an important aspect in HIV eradication efforts. The urinary tract has however not been well studied as a potential HIV reservoir. In this pilot study we molecularly characterized HIV-1 viruses in urine and plasma samples to investigate HIV-1 replication, compartmentalization and persistence in the urinary tract. METHODS:Prospectively collected urine and blood samples collected over 12-36 months from 20 HIV-1 infected individuals were analysed including sampling points from prior to and after ART initiation. HIV-1 pol gene RNA and DNA from urine supernatant and urine pellets respectively were analysed and compared to plasma RNA viruses from the same individual. RESULTS:HIV-1 nucleic acid was detected in urine samples from at least one time point in 8/20 (40%) treatment-naïve subjects compared to 1/13 (7.7%) individuals on antiretroviral treatment (ART) during periods of plasma viral suppression and 1/7 (14.3%) individuals with virological failure. HIV-1 RNA was undetectable in urine samples after ART initiation but HIV-1 DNA was detectable in one patient more than 6 months after treatment initiation. There was co-clustering of urine-derived pol sequences but some urine-derived sequences were interspersed among the plasma-derived sequences. CONCLUSIONS:Suppressive ART reduces HIV-1 replication in the urinary tract but HIV-1 DNA may persist in these cells despite treatment. A larger number of sequences would be required to confirm HIV compartmentalization in the urinary tract.

| S-EPMC6760049 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data