Identification of groups of metabolically-active rhizosphere microorganisms by stable isotope probing of PLFAs

Treonis, Amy M.; Ostle, Nicholas J.; Stott, Andrew; Primrose, Ruth; Grayston, Susan J.; Ineson, P.

doi:10.1016/j.soilbio.2003.10.015

Cited by 221 publications

(155 citation statements)

References 20 publications

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“…The detection of differences between taxa with quantitative stable isotope probing (ϳ0.05 atom fraction excess) is 4 orders of magnitude less precise than that achieved with gas isotope ratio analysis of bulk organic matter in continuous flow, where differences of 0.000005 atom fraction excess or better (Ͻ0.5‰) can be resolved (44). Isopycnic centrifugation to quantify isotope composition is also less precise than compound-specific analysis of biomarkers, for example, of 13 C in fatty acids, where resolution of 0.00002 atom fraction excess (or 2‰) is typical (45)(46)(47). Coupling stable isotope tracing with nanoscale secondary ion mass spectrometry (Nano-SIMS) and microarrays, a coupling called Chip-SIP (48), can resolve 0.005 atom fraction excess for 15 N and 0.001 for 13 C (49), considerably more precise than qSIP.…”

Section: Discussionmentioning

confidence: 95%

Quantitative Microbial Ecology through Stable Isotope Probing

Hungate

Mau

Schwartz

et al. 2015

Appl Environ Microbiol

259

313

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Bacteria grow and transform elements at different rates, and as yet, quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to stable isotope probing (SIP) that enables the isotopic composition of DNA from individual bacterial taxa after exposure to isotope tracers to be determined. In our modification, after isopycnic centrifugation, DNA is collected in multiple density fractions, and each fraction is sequenced separately. Taxon-specific density curves are produced for labeled and nonlabeled treatments, from which the shift in density for each individual taxon in response to isotope labeling is calculated. Expressing each taxon's density shift relative to that taxon's density measured without isotope enrichment accounts for the influence of nucleic acid composition on density and isolates the influence of isotope tracer assimilation. The shift in density translates quantitatively to isotopic enrichment. Because this revision to SIP allows quantitative measurements of isotope enrichment, we propose to call it quantitative stable isotope probing (qSIP). We demonstrated qSIP using soil incubations, in which soil bacteria exhibited strong taxonomic variations in 18

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Section: Discussionmentioning

confidence: 95%

Quantitative Microbial Ecology through Stable Isotope Probing

Hungate

Mau

Schwartz

et al. 2015

Appl Environ Microbiol

259

313

View full text Add to dashboard Cite

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“…Previous studies have identified Pseudomonas and Burkholderia as highly rhizo-competent genera (Vancanneyt et al, 1996;Lugtenberg et al, Responses of specific rhizosphere microbial communities to elevated CO 2 B Drigo et al 2001; Treonis et al, 2004;Berg et al, 2005). In contrast, actinomycetes and Bacillus spp.…”

Section: Discussionmentioning

confidence: 99%

Specific rhizosphere bacterial and fungal groups respond differently to elevated atmospheric CO2

2009

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Soil community responses to increased atmospheric CO 2 concentrations are expected to occur mostly through interactions with changing vegetation patterns and plant physiology. To gain insight into the effects of elevated atmospheric CO 2 on the composition and functioning of microbial communities in the rhizosphere, Carex arenaria (a non-mycorrhizal plant species) and Festuca rubra (a mycorrhizal plant species) were grown under defined atmospheric conditions with either ambient (350 p.p.m.) or elevated (700 p.p.m.) CO 2 concentrations. PCR-DGGE (PCR-denaturing gradient gel electrophoresis) and quantitative-PCR were carried out to analyze, respectively, the structure and abundance of the communities of actinomycetes, Fusarium spp., Trichoderma spp., Pseudomonas spp., Burkholderia spp. and Bacillus spp. Responses of specific functional groups, such as phloroglucinol, phenazine and pyrrolnitrin producers, were also examined by quantitative-PCR, and HPLC (high performance liquid chromatography) was employed to assess changes in exuded sugars in the rhizosphere. Multivariate analysis of group-specific community profiles showed disparate responses to elevated CO 2 for the different bacterial and fungal groups examined, and these responses were dependent on plant type and soil nutrient availability. Within the bacterial community, the genera Burkholderia and Pseudomonas, typically known as successful rhizosphere colonizers, were significantly influenced by elevated CO 2 , whereas the genus Bacillus and actinomycetes, typically more dominant in bulk soil, were not. Total sugar concentrations in the rhizosphere also increased in both plants in response to elevated CO 2 . The abundances of phloroglucinol-, phenazine-and pyrrolnitrin-producing bacterial communities were also influenced by elevated CO 2 , as was the abundance of the fungal genera Fusarium and Trichoderma.

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“…It has been shown previously that fungal species tend to be primary feeders at the expense of autotrophic metabolism within the rhizosphere (Butler et al, 2003;Jin and Evans, 2010) prior to widespread degradation of biomass and exudates by the remaining microbiological community. The lack of enrichment and low mass of polyenoic fatty acids for the sampling events, indicates a limited input of plant-and possibly protazoan- (Vestle and White, 1989;Rønn et al, 2002;Treonis et al, 2004) derived fatty acids.…”

Section: Isotopic Labelling Incubationsmentioning

confidence: 99%

CO2 uptake by a soil microcosm

Hart

Oppenheimer

Moran

et al. 2013

Soil Biology and Biochemistry

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CO 2 enrichment a b s t r a c t Sequestration of CO 2 via biological sinks is a matter of great scientific importance due to the potential lowering of atmospheric CO 2 . In this study, a custom built incubation chamber was used to cultivate a soil microbial community to instigate chemoautotrophy of a temperate soil. Real-time atmospheric CO 2 concentrations were monitored and estimations of total CO 2 uptake were made. After careful background flux corrections, 4.52 AE 0.05 g CO 2 kg À1 dry soil was sequestered from the chamber atmosphere over 40 h. Using isotopically labelled 13 CO 2 and GCMSeIRMS, labelled fatty acids were identified after only a short incubation, hence confirming CO 2 sequestration for soil. The results of this in vivo study provide the ground work for future studies intending to mimic the in situ environment by providing a reliable method for investigating CO 2 uptake by soil microorganisms.

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Identification of groups of metabolically-active rhizosphere microorganisms by stable isotope probing of PLFAs

Cited by 221 publications

References 20 publications

Quantitative Microbial Ecology through Stable Isotope Probing

Quantitative Microbial Ecology through Stable Isotope Probing

Specific rhizosphere bacterial and fungal groups respond differently to elevated atmospheric CO2

CO2 uptake by a soil microcosm

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