DNA stable-isotope probing

Whiteley, Andrew S.; Thomson, Bruce C.; Lueders, Tillmann; Manefield, Mike

doi:10.1038/nprot.2007.109

Cited by 446 publications

(417 citation statements)

References 14 publications

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“…pore-size polycarbonate filters (Whatman). DNA was subsequently extracted using a protocol adapted from Fuller et al (2003) and Neufeld et al (2007). Briefly, cells were resuspended in 50 ml lysis buffer (0.75 M sucrose, 400 mM NaCl, 20 mM EDTA, 50 mM Tris-HCl [pH 9.0]-Sigma-Aldrich), and then 6 ml 10% (w/v) sodium dodecyl sulphate, 10 ml 10 mg ml À1 proteinase K (Roche, Welwyn Garden City, UK) added.…”

Section: Chrysophyte Probe Validation and Optimization For Whole-cellmentioning

confidence: 99%

Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean

et al. 2010

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Global estimates indicate the oceans are responsible for approximately half of the carbon dioxide fixed on Earth. Organisms p5 lm in size dominate open ocean phytoplankton communities in terms of abundance and CO 2 fixation, with the cyanobacterial genera Prochlorococcus and Synechococcus numerically the most abundant and more extensively studied compared with small eukaryotes. However, the contribution of specific taxonomic groups to marine CO 2 fixation is still poorly known. In this study, we show that among the phytoplankton, small eukaryotes contribute significantly to CO 2 fixation (44%) because of their larger cell volume and thereby higher cell-specific CO 2 fixation rates. Within the eukaryotes, two groups, herein called Euk-A and Euk-B, were distinguished based on their flow cytometric signature. Euk-A, the most abundant group, contained cells 1.8±0.1 lm in size while Euk-B was the least abundant but cells were larger (2.8±0.2 lm). The Euk-B group comprising prymnesiophytes (73±13%) belonging largely to lineages with no close cultured counterparts accounted for up to 38% of the total primary production in the subtropical and tropical northeast Atlantic Ocean, suggesting a key role of this group in oceanic CO 2 fixation.

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Section: Chrysophyte Probe Validation and Optimization For Whole-cellmentioning

confidence: 99%

Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean

et al. 2010

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“…13 C-enriched ('heavy') DNA was separated from non-labeled ('light') 119 DNA by density-gradient centrifugation and analysed as described in Neufeld et al (2007). Fungal PCR was 120 performed for combined 'heavy' and 'light' fractions using primers ITS4 and ITS9 (Ihrmark et al 2012 The relative labeling of each OTU was determined as the ratio of the abundance of that OTU in the heavy 139 13 C fraction to that of the abundance in the light 12 C fraction 140…”

Section: Plfa and Nlfa Analysis 111mentioning

confidence: 99%

Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture

et al. 2017

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21Activities of rhizosphere microbes are key to the functioning of terrestrial ecosystems. It is commonly 22 believed that bacteria are the major consumers of root exudates and that the role of fungi is thought to 23 be limited to that of mycorrhizae and pathogens. In order to test the hypothesis that the role of 24 saprotrophic fungi in rhizosphere processes increases with increased time after abandonment from 25 agriculture, we determined the composition of fungi that are active in the rhizosphere along a 26 chronosequence of ex-arable fields in The Netherlands. Intact soil cores were collected from nine fields 27 that represent three stages of land abandonment and pulse labelled with 13 CO2. The fungal contribution 28 to metabolizing plant-derived carbon was evaluated using phospholipid analysis combined with stable 29

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“…To separate the labelled ( 13 C) and unlabelled ( 12 C) DNA, the procedure of Neufeld et al (2007) was used. Separation was achieved by using density gradient fractionation of the total DNA extract (50 mL) on a CsCl gradient with a buoyant density of 1.725 g ml À 1 that was subjected to ultracentrifugation in a Sorvall 100SE Ultracentrifuge (Thermo Scientific, Loughborough, UK) at 44 100 r.p.m.…”

Section: Dna-stable-isotope Probingmentioning

confidence: 99%

Stable-isotope probing and metagenomics reveal predation by protozoa drives E. coli removal in slow sand filters

et al. 2014

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Stable-isotope probing and metagenomics were applied to study samples taken from laboratoryscale slow sand filters 0.5, 1, 2, 3 and 4 h after challenging with 13 C-labelled Escherichia coli to determine the mechanisms and organisms responsible for coliform removal. Before spiking, the filters had been continuously operated for 7 weeks using water from the River Kelvin, Glasgow as their influent source. Direct counts and quantitative PCR assays revealed a clear predator-prey response between protozoa and E. coli. The importance of top-down trophic-interactions was confirmed by metagenomic analysis, identifying several protozoan and viral species connected to E. coli attrition, with protozoan grazing responsible for the majority of the removal. In addition to top-down mechanisms, indirect mechanisms, such as algal reactive oxygen species-induced lysis, and mutualistic interactions between algae and fungi, were also associated with coliform removal. The findings significantly further our understanding of the processes and trophic interactions underpinning E. coli removal. This study provides an example for similar studies, and the opportunity to better understand, manage and enhance E. coli removal by allowing the creation of more complex trophic interaction models.

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DNA stable-isotope probing

Cited by 446 publications

References 14 publications

Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean

Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean

Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture

Stable-isotope probing and metagenomics reveal predation by protozoa drives E. coli removal in slow sand filters

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