Who eats what, where and when? Isotope-labelling experiments are coming of age

Neufeld, Josh D.; Wagner, Michael; Murrell, J. Colin

doi:10.1038/ismej.2007.30

Cited by 240 publications

(161 citation statements)

References 66 publications

(75 reference statements)

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“…Single-cell amplification Microbial ecology is in the early stages of establishing links between uncultivated microorganisms in the environment and their trophic roles within communities (Neufeld et al, 2007). Progress has been made in the ability to analyze genomes, without the prerequisite of cultivation, by using MDA from individual cells.…”

Section: Use Of Mda In Microbial Ecologymentioning

confidence: 99%

“…Stable isotope probing (SIP) is a powerful method that establishes this link between function and phylogeny (Neufeld et al, 2007); however, it has been limited by an experimental 'catch-22'. Does one add an excess of labelled substrate to an SIP incubation to increase the yield of labelled DNA and potentially bias the experiment toward copiotrophic species capable of rapid cell division?…”

Section: Whole Community Genome Amplificationmentioning

confidence: 99%

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Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology

2008

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Microbial ecology is a field that applies molecular techniques to analyze genes and communities associated with a plethora of unique environments on this planet. In the past, low biomass and the predominance of a few abundant community members have impeded the application of techniques such as PCR, microarray analysis and metagenomics to complex microbial populations. In the absence of suitable cultivation methods, it was not possible to obtain DNA samples from individual microorganisms. Recently, a method called multiple displacement amplification (MDA) has been used to circumvent these limitations by amplifying DNA from microbial communities in low-biomass environments, individual cells from uncultivated microbial species and active organisms obtained through stable isotope probing incubations. This review describes the development and applications of MDA, discusses its strengths and limitations and highlights the impact of MDA on the field of microbial ecology. Whole genome amplification via MDA has increased access to the genomic DNA of uncultivated microorganisms and low-biomass environments and represents a 'power tool' in the molecular toolbox of microbial ecologists.

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Section: Use Of Mda In Microbial Ecologymentioning

confidence: 99%

Section: Whole Community Genome Amplificationmentioning

confidence: 99%

Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology

2008

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“…The recent development of stable isotope probing (SIP) (Radajewski et al, 2000) and its application to tracking plant-derived C into microbial nucleic acids (Rangel-Castro et al, 2005;Lu et al, 2006;Prosser et al, 2006;Neufeld et al, 2007) or other biochemical markers (Treonis et al, 2004;Paterson et al, 2007) provide the opportunity to understand the functional diversity of plant-associated bacterial communities.…”

Section: Introductionmentioning

confidence: 99%

Plant host habitat and root exudates shape soil bacterial community structure

et al. 2008

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The rhizosphere is active and dynamic in which newly generated carbon, derived from root exudates, and ancient carbon, in soil organic matter (SOM), are available for microbial growth. Stable isotope probing (SIP) was used to determine bacterial communities assimilating each carbon source in the rhizosphere of four plant species. Wheat, maize, rape and barrel clover (Medicago truncatula) were grown separately in the same soil under 13 CO 2 (99% of atom 13 C) and DNA extracted from rhizosphere soil was fractionated by isopycnic centrifugation. Bacteria-assimilating root exudates were characterized by denaturing gradient gel electrophoresis (DGGE) analysis of 13 C-DNA and root DNA, whereas those assimilating SOM were identified from 12 C-DNA. Plant species root exudates significantly shaped rhizosphere bacterial community structure. Bacteria related to Sphingobacteriales and Myxococcus assimilated root exudates in colonizing roots of all four plants, whwereas bacteria related to Sphingomonadales utilized both carbon sources, and were identified in light, heavy and root compartment DNA. Sphingomonadales were specific to monocotyledons, whereas bacteria related to Enterobacter and Rhizobiales colonized all compartments of all four plants, used both fresh and ancient carbon and were considered as generalists. There was also evidence for an indirect important impact of root exudates, through stimulation of SOM assimilation by a diverse bacterial community.

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“…A combination of molecular biological tools (McDonald et al, 2008) and stable isotope labeling of lipids (Boschker et al, 1998;Neufeld et al, 2007) and proteins (Seifert et al, 2012) is applied to exploit the characteristics of aerobic MOB to serve as a model group in microbial BEF studies in the most optimal way. More specifically, we want to investigate the role of available niches on the diversity-functioning relationship by assessing the active MOB community members in a spatial and temporal investigation carried out in a riparian floodplain that is characterized by a natural gradient of hydrological conditions providing a variable amount of niches for MOB.…”

Section: Introductionmentioning

confidence: 99%

Microbial minorities modulate methane consumption through niche partitioning

et al. 2013

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Microbes catalyze all major geochemical cycles on earth. However, the role of microbial traits and community composition in biogeochemical cycles is still poorly understood mainly due to the inability to assess the community members that are actually performing biogeochemical conversions in complex environmental samples. Here we applied a polyphasic approach to assess the role of microbial community composition in modulating methane emission from a riparian floodplain. We show that the dynamics and intensity of methane consumption in riparian wetlands coincide with relative abundance and activity of specific subgroups of methane-oxidizing bacteria (MOB), which can be considered as a minor component of the microbial community in this ecosystem. Microarray-based community composition analyses demonstrated linear relationships of MOB diversity parameters and in vitro methane consumption. Incubations using intact cores in combination with stable isotope labeling of lipids and proteins corroborated the correlative evidence from in vitro incubations demonstrating c-proteobacterial MOB subgroups to be responsible for methane oxidation. The results obtained within the riparian flooding gradient collectively demonstrate that niche partitioning of MOB within a community comprised of a very limited amount of active species modulates methane consumption and emission from this wetland. The implications of the results obtained for biodiversity-ecosystem functioning are discussed with special reference to the role of spatial and temporal heterogeneity and functional redundancy.

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Who eats what, where and when? Isotope-labelling experiments are coming of age

Cited by 240 publications

References 66 publications

Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology

Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology

Plant host habitat and root exudates shape soil bacterial community structure

Microbial minorities modulate methane consumption through niche partitioning

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