Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes

ABSTRACT: Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes

PROVIDER: PRJNA152479 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR407413.fastq.gz	Fastqsanger.gz
	SRR407414.fastq.gz	Fastqsanger.gz
	SRR407415.fastq.gz	Fastqsanger.gz
	SRR407416.fastq.gz	Fastqsanger.gz
	SRR407417.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes

Project description:The characterization of microbial community structure via 16S rRNA gene profiling has been greatly advanced in recent years by the application of amplicon pyrosequencing. The possibility of barcode-tagged sequencing of templates gives the opportunity to massively screen multiple samples from environmental or clinical sources for community details. However, an on-going debate questions the reproducibility and semi-quantitative rigour of pyrotag sequencing and, as in the early days of genetic community fingerprinting, pros and cons are continuously provided. In this study we investigate the reproducibility of bacterial 454 pyrotag sequencing over biological and technical replicates of natural microbiota. Moreover, via quantitatively defined template spiking to the natural community, we explore the potential for recovering specific template ratios within complex microbial communities. For this reason, we pyrotag sequenced three biological replicates of three samples, each belonging from yearly sampling campaigns of sediment from a tar oil contaminated aquifer in Düsseldorf, Germany. Furthermore, we subjected one DNA extract to replicate technical analyses as well as to increasing ratios (0, 0.2, 2 and 20%) of 16S rRNA genes from a pure culture (Aliivibrio fisheri) originally not present in the sample. Unexpectedly, taxa abundances were highly reproducible in our hands, with max standard deviation of ~3% abundance across biological and ~2% for technical replicates. Furthermore, our workflow was also capable of recovering A. fisheri amendmend ratios in reliable amounts (0, 0.29, 3.9 and 23.8%). These results highlight that pyrotag sequencing, if done and evaluated with due caution, has the potential to robustly recapture taxa template abundances within environmental microbial communities. 9 Biological and 3 technical replicates were evaluated, as well as potential to recover qPCR-defined ratios of DNA, in 454 pyrotag sequencing

2012-07-16 | E-GEOD-35631 | biostudies-arrayexpress

Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes

2012-07-16 | GSE35631 | GEO

Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes.

Project description:The characterization of microbial community structure via 16S rRNA gene profiling has been greatly advanced in recent years by the introduction of amplicon pyrosequencing. The possibility of barcoding gives the opportunity to massively screen multiple samples from environmental or clinical sources for community details. However, an on-going debate questions the reproducibility and semi-quantitative rigour of pyrotag sequencing, similar to the early days of community fingerprinting. In this study we demonstrate the reproducibility of bacterial 454 pyrotag sequencing over biological and technical replicates of aquifer sediment bacterial communities. Moreover, we explore the potential of recovering specific template ratios via quantitatively defined template spiking to environmental DNA. We sequenced pyrotag libraries of triplicate sediment samples taken in annual sampling campaigns at a tar oil contaminated aquifer in Düsseldorf, Germany. The abundance of dominating lineages was highly reproducible with a maximal standard deviation of ~4% read abundance across biological, and ~2% across technical replicates. Our workflow also allows for the linking of read abundances within defined assembled pyrotag contigs to that of specific 'in vivo' fingerprinting signatures. Thus we demonstrate that both terminal restriction fragment length polymorphism (T-RFLP) analysis and pyrotag sequencing are capable of recovering highly comparable community structure. Overall diversity was roughly double in amplicon sequencing. Pyrotag libraries were also capable of linearly recovering increasing ratios (up to 20%) of 16S rRNA gene amendments from a pure culture of Aliivibrio fisheri spiked to sediment DNA. Our study demonstrates that 454 pyrotag sequencing is a robust and reproducible method, capable of reliably recovering template abundances and overall community structure within natural microbial communities.

| S-EPMC3395703 | biostudies-literature

Expression analysis in anaerobic Hanford 100H aquifer flow-through columns receiving lactate and chromate

Project description:Columns containing Hanford 100H aquifer sediment continuously infused with 5 mM lactate, 5 uM Cr(VI), and either 7.5 mM sulfate or 12 mM nitrate as an electron acceptor.

2014-04-08 | GSE56554 | GEO

Transcriptome-stable isotope probing provides targeted functional and taxonomic insights into hypoxic pollutant-degrading aquifer microbiota

Project description:We investigated a contaminant-degrading microbial community by sequencing total RNA (without rRNA depletion) from microcosms containing sediment from a hypoxic contaminated aquifer fed with isotopically labeled toluene.

2018-09-07 | GSE119644 | GEO

Aquifer

Project description:Aquifer Raw sequence reads

| PRJNA509748 | ENA

Aquifer metaproteomics - Candidate Brocadiales dominates C, N and S cycling in anoxic groundwater of a pristine limestone-fracture aquifer

Project description:Groundwater-derived microorganisms are known to play an important role in biogeochemical C, S and N cycling. Thereby, the presence and majorly the activity of microorganisms in aquifers affect enormously the nutrient cycling. However, the diversity and their functional capability in natural aquifers are still rare and therefore a better knowledge of the core microbial communities is urgently needed. Metaproteome analysis was applied to characterize the repertoire of microbes in the depth and to identify the key drivers of major biogeochemical processes. Therefore, 1000 L water from the aquifer was sampled by filtration on 0.3 µm glass filters. After protein extraction, proteolytic cleavage and mass spectrometric analysis (Ultimate 3000 nanoRSLC coupled to Q Exactive HF instrument), 3808 protein groups (2371 proteins with ≥2 peptides) were identified from 13,204 peptides. The findings of our study have broad implications for the understanding of aquifer cycling’s which finally leads to a greatly improved understanding of the ecosystem services provided by the microbial communities present in aquifers. In the future, functional results would allow to monitor and to assess pollution effects which would beneficially assist groundwater resource management.

2016-12-23 | PXD004351 | Pride

aquifer metagenome

Project description:aquifer metagenome Metagenome

| PRJNA340364 | ENA

Aquifer material

Project description:Aquifer material Metagenome

| PRJNA720508 | ENA

Hellisheidi aquifer

Project description:Hellisheidi aquifer Metagenome

| PRJNA1085311 | ENA