ArticleApplied and environmental microbiology2009
Linking microbial community function to phylogeny of sulfate-reducing Deltaproteobacteria in marine sediments by combining stable isotope probing with magnetic-bead capture hybridization of 16S rRNA.
Article in Applied and environmental microbiology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 49 citations in OpenAlex.
- Tracing microbial carbon sources in hydrothermal sediments byFrontiers in microbiology · 2025Article
- Variations in bacterial and archaeal community structure and diversity along the soil profiles of a peatland in Southwest China.Environmental science and pollution research international · 2022Article
- A Cross-System Comparison of Dark Carbon Fixation in Coastal Sediments.Global biogeochemical cycles · 2020Article
- Microbial Composition and Variability of Natural Marine Planktonic and Biofouling Communities From the Bay of Bengal.Frontiers in microbiology · 2019Article
- UnculturedFrontiers in microbiology · 2018Article
- Rhizosphere bacterial carbon turnover is higher in nucleic acids than membrane lipids: implications for understanding soil carbon cycling.Frontiers in microbiology · 2015Article
- The "Oil-Spill Snorkel": an innovative bioelectrochemical approach to accelerate hydrocarbons biodegradation in marine sediments.Frontiers in microbiology · 2015Article
- RNA-stable-isotope probing shows utilization of carbon from inulin by specific bacterial populations in the rat large bowel.Applied and environmental microbiology · 2014Article
- Microfluidic platform for isolating nucleic acid targets using sequence specific hybridization.Biomicrofluidics · 2013Article
- Depth-related differences in organic substrate utilization by major microbial groups in intertidal marine sediment.Applied and environmental microbiology · 2013Article
- Abundance, diversity and activity of sulfate-reducing prokaryotes in heavy metal-contaminated sediment from a salt marsh in the Medway Estuary (UK).Marine biotechnology (New York, N.Y.) · 2012Article
- Use of stable isotopes to measure the metabolic activity of the human intestinal microbiota.Applied and environmental microbiology · 2011Article
- Toward understanding, managing, and protecting microbial ecosystems.Frontiers in microbiology · 2011Article
- From structure to function: the ecology of host-associated microbial communities.Microbiology and molecular biology reviews : MMBR · 2010Review
- Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation.Biotechnology advancesReview
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We further developed the stable isotope probing, magnetic-bead capture method to make it applicable for linking microbial community function to phylogeny at the class and family levels. The main improvements were a substantial decrease in the protocol blank and an approximately 10-fold increase in the detection limit by using a micro-elemental analyzer coupled to isotope ratio mass spectrometry to determine (13)C labeling of isolated 16S rRNA. We demonstrated the method by studying substrate utilization by Desulfobacteraceae, a dominant group of complete oxidizing sulfate-reducing Deltaproteobacteria in marine sediments. Stable-isotope-labeled [(13)C]glucose, [(13)C]propionate, or [(13)C]acetate was fed into an anoxic intertidal sediment. We applied a nested set of three biotin-labeled oligonucleotide probes to capture Bacteria, Deltaproteobacteria, and finally Desulfobacteraceae rRNA by using hydrophobic streptavidin-coated paramagnetic beads. The target specificities of the probes were examined with pure cultures of target and nontarget species and by determining the phylogenetic composition of the captured sediment rRNA. The specificity of the final protocol was generally very good, as more than 90% of the captured 16S rRNA belonged to the target range of the probes. Our results indicated that Desulfobacteraceae were important consumers of propionate but not of glucose. However, the results for acetate utilization were less conclusive due to lower and more variable labeling levels in captured rRNA. The main advantage of the method in this study over other nucleic acid-based stable isotope probing methods is that (13)C labeling can be much lower, to the extent that delta(13)C ratios can be studied even at their natural abundances.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.