Rapid resonance Raman microspectroscopy to probe carbon dioxide fixation by single cells in microbial communities

Li, Mengqiu; Canniffe, Daniel P.; Jackson, Philip J.; Davison, Paul A.; FitzGerald, Simon; Dickman, Mark J.; Burgess, J. Grant; Hunter, C. Neil; Huang, Wei E.

doi:10.1038/ismej.2011.150

Cited by 99 publications

(135 citation statements)

References 43 publications

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“…Raman microspectroscopy has often been used to characterize spatial distribution and molecular composition of biological samples (Wagner, 2009;Beier et al, 2010;Hall et al, 2011;Li et al, 2012). However, to date, Raman microscopy has often been used together with FISH (Raman-FISH) to differentiate microbial populations such as Bacteria and Archaea (Huang et al, 2007).…”

Section: Discussionmentioning

confidence: 99%

Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm

et al. 2012

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Archaea are usually minor components of a microbial community and dominated by a large and diverse bacterial population. In contrast, the SM1 Euryarchaeon dominates a sulfidic aquifer by forming subsurface biofilms that contain a very minor bacterial fraction (5%). These unique biofilms are delivered in high biomass to the spring outflow that provides an outstanding window to the subsurface. Despite previous attempts to understand its natural role, the metabolic capacities of the SM1 Euryarchaeon remain mysterious to date. In this study, we focused on the minor bacterial fraction in order to obtain insights into the ecological function of the biofilm. We link phylogenetic diversity information with the spatial distribution of chemical and metabolic compounds by combining three different state-of-the-art methods: PhyloChip G3 DNA microarray technology, fluorescence in situ hybridization (FISH) and synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy. The results of PhyloChip and FISH technologies provide evidence for selective enrichment of sulfate-reducing bacteria, which was confirmed by the detection of bacterial dissimilatory sulfite reductase subunit B (dsrB) genes via quantitative PCR and sequence-based analyses. We further established a differentiation of archaeal and bacterial cells by SR-FTIR based on typical lipid and carbohydrate signatures, which demonstrated a co-localization of organic sulfate, carbonated mineral and bacterial signatures in the biofilm. All these results strongly indicate an involvement of the SM1 euryarchaeal biofilm in the global cycles of sulfur and carbon and support the hypothesis that sulfidic springs are important habitats for Earth's energy cycles. Moreover, these investigations of a bacterial minority in an Archaea-dominated environment are a remarkable example of the great power of combining highly sensitive microarrays with label-free infrared imaging.

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Section: Discussionmentioning

confidence: 99%

Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm

et al. 2012

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“…These techniques involve irradiating a sample with specific wavelengths of light and measuring light scattering (Raman spectroscopy) or absorbance (FTIR spectroscopy) by the sample. The resulting spectra consist of absorbance bands associated with macromolecules that can be interpreted to reveal quantitative variations in cell phenotype in terms of physiology (Li et al, 2012), pigment content (Andreeva and Velitchkova, 2005) and macromolecular composition (Heraud, et al, 2007b). In a recent study, Jebsen et al (2012) predicted growth rates from FTIR spectra of microalgal cells, showing that FTIR spectroscopy can provide a valuable alternative to time-series measurements for the collection of physiological rate data.…”

Section: Introductionmentioning

confidence: 99%

Snapshot prediction of carbon productivity, carbon and protein content in a Southern Ocean diatom using FTIR spectroscopy

et al. 2015

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Diatoms, an important group of phytoplankton, bloom annually in the Southern Ocean, covering thousands of square kilometers and dominating the region's phytoplankton communities. In their role as the major food source to marine grazers, diatoms supply carbon, nutrients and energy to the Southern Ocean food web. Prevailing environmental conditions influence diatom phenotypic traits (for example, photophysiology, macromolecular composition and morphology), which in turn affect the transfer of energy, carbon and nutrients to grazers and higher trophic levels, as well as oceanic biogeochemical cycles. The paucity of phenotypic data on Southern Ocean phytoplankton limits our understanding of the ecosystem and how it may respond to future environmental change. Here we used a novel approach to create a 'snapshot' of cell phenotype. Using mass spectrometry, we measured nitrogen (a proxy for protein), total carbon and carbon-13 enrichment (carbon productivity), then used this data to build spectroscopy-based predictive models. The models were used to provide phenotypic data for samples from a third sample set. Importantly, this approach enabled the first ever rate determination of carbon productivity from a single time point, circumventing the need for timeseries measurements. This study showed that Chaetoceros simplex was less productive and had lower protein and carbon content during short-term periods of high salinity. Applying this new phenomics approach to natural phytoplankton samples could provide valuable insight into understanding phytoplankton productivity and function in the marine system.

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“…Typical examples involve the use of a UV excitation laser to detect the resonant Raman spectra of amino or nucleic acids (Asher, 1988; Puppels et al, 1991). Due to the presence of autofluorescent compounds/pigments, resonance Raman has been particularly useful in the biochemical and metabolic studies of photosynthetic microorganisms (Li et al, 2012). Recently, the dynamics of cytochrome c under physiological and stress conditions were studied by resonance Raman, revealing its role in cell apoptosis (Okada et al, 2012).…”

Section: Probing Single Cellsmentioning

confidence: 99%

Review of methods to probe single cell metabolism and bioenergetics

Vasdekis

Stephanopoulos

2015

Metabolic Engineering

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Single cell investigations have enabled unexpected discoveries, such as the existence of biological noise and phenotypic switching in infection, metabolism and treatment. Herein, we review methods that enable such single cell investigations specific to metabolism and bioenergetics. Firstly, we discuss how to isolate and immobilize individuals from a cell suspension, including both permanent and reversible approaches. We also highlight specific advances in microbiology for its implications in metabolic engineering. Methods for probing single cell physiology and metabolism are subsequently reviewed. The primary focus therein is on dynamic and high-content profiling strategies based on label-free and fluorescence microspectroscopy and microscopy. Non-dynamic approaches, such as mass spectrometry and nuclear magnetic resonance, are also briefly discussed.

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Rapid resonance Raman microspectroscopy to probe carbon dioxide fixation by single cells in microbial communities

Cited by 99 publications

References 43 publications

Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm

Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm

Snapshot prediction of carbon productivity, carbon and protein content in a Southern Ocean diatom using FTIR spectroscopy

Review of methods to probe single cell metabolism and bioenergetics

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