Single cell activity reveals direct electron transfer in methanotrophic consortia (original) (raw)

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Data deposits

Sequence for the ANME-2b multi-haem cytochrome protein was deposited in GenBank under the accession number KR811028.

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Acknowledgements

We are grateful for the use of the facilities of the Beckman Resource Center for Transmission Electron Microscopy at Caltech (BRCem) and advice provided by A. McDowall, our collaborators T. Deerinck and M. Ellisman from the National Center for Microscopy and Imaging Research (NCMIR), C. Miele (UGA) and M. El-Naggar at USC. Metagenomic binning of ANME-2b was conducted by C. Skennerton and M. Haroon in collaboration with G. Tyson and M. Imelfort (University of Queensland). This work was supported by the US Department of Energy, Office of Science, Office of Biological Environmental Research under award numbers (DE-SC0004949 and DE-SC0010574) and a grant from the Gordon and Betty Moore foundation Marine Microbiology Initiative (grant number 3780). V.J.O. is supported by a DOE-BER early career grant (DE-SC0003940). S.E.M. acknowledges support from an Agouron Geobiology Option post-doctoral fellowship in the Division of Geological and Planetary Sciences at Caltech and C.P.K. was supported by the NASA Astrobiology Institute (award number NNA13AA92A). This is NAI-Life Underground Publication 049.

Author information

Author notes

  1. Shawn E. McGlynn
    Present address: †Present address: Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan.,
  2. Shawn E. McGlynn and Grayson L. Chadwick: These authors contributed equally to this work.

Authors and Affiliations

  1. Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, 91125, California, USA
    Shawn E. McGlynn, Grayson L. Chadwick & Victoria J. Orphan
  2. Exobiology Branch, National Aeronautics and Space Administration Ames Research Center, Moffett Field, 94035, California, USA
    Christopher P. Kempes
  3. Control and Dynamical Systems, California Institute of Technology, Pasadena, 91125, California, USA
    Christopher P. Kempes
  4. SETI Institute, Mountain View, 94034, California, USA
    Christopher P. Kempes

Authors

  1. Shawn E. McGlynn
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  2. Grayson L. Chadwick
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  3. Christopher P. Kempes
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  4. Victoria J. Orphan
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Contributions

V.J.O., S.M. and G.L.C. devised the study, S.M. and G.L.C. conducted the experiments and analyses and C.P.K. conducted the diffusion and electrical conductivity modelling, and all authors contributed to data interpretation and writing of the manuscript.

Corresponding author

Correspondence toVictoria J. Orphan.

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Competing interests

The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Image processing workflow for single cell correlation between FISH and nanoSIMS data sets.

Representative example of data processing for an AOM consortium. a, Fiducial markers added to the FISH image. Marker points are shown in yellow, bacterial cells in red, archaeal cells in green. b, Corresponding fiducial markers identified on the nanoSIMS image. c, Overlay of the warped FISH image onto the nanoSIMS image, the transform function was defined by the points shown in a and b. d, Overlay of the original FISH image (yellow) and the warped FISH image (blue) highlighting a slight offset which becomes significant at single-cell resolutions. e, Centroids of the hand-drawn ROIs displayed on the nanoSIMS image, bacteria in red, archaea in green. f, Inverse transform applied to the ROIs drawn on the nanoSIMS image, bringing the centroid coordinates into ‘FISH space’ where we have more accurate measurement of distances between points.

Extended Data Figure 2 Spatial and geometric relationships for modelled aggregate geometries (well mixed to segregated) as a function of relative diffusivity (the ratio of growth rates to growth yields and diffusivity; see Supplementary Information) within the intermediate exchange model.

Slow diffusion is on the left (equivalent to roughly half the relative diffusivity of hydrogen compared to measured growth rates in our system) and fast on the right (equivalent to 103 times faster relative diffusivity than hydrogen compared with measured growth rates; see Supplementary Information). a, Total aggregate activity normalized to the group maximum as a function of the J spatial metric showing a strong dependency on geometry favouring well mixed (low J value) geometries under slow relative diffusion (left) and almost no relationship with J in fast-diffusion models (right). The average activity, normalized across all of the regimes rather than within a single regime, also changes dramatically from 0.002 to 0.99 as the relative diffusivity is increased. b, Total normalized archaeal population activity plotted against the total bacterial population activity within the same modelled aggregate. The total number of in silico consortia for rows a and b is 23. c, The normalized (_z_-score) activity for archaea (red) and bacteria (green) plotted against the distance to the nearest three partners. d, The _z_-score activity for archaea (green) and bacteria (red) plotted against the distance to environment-aggregate interface (that is, aggregate surface). In plots c and d the _r_-squared values for each correlation are given at the top of each plot in colours that correspond to the two cell types. The number of modelled in silico bacterial and archaeal cells from c and d plotted in the columns from left to right are: 1,138 bacterial and 1,162 archaeal cells; 1,163 bacterial and 1,137 archaeal cells; and 1,153 bacterial and 1,147 archaeal cells. As diffusion is increased in these models from left to right, the organisms within consortia become less dependent on each other and instead become less syntrophically coupled, relying on environmental exchange. This leads to the highest average activity rates per consortia (compare the top panel a to b).

Extended Data Figure 3 Summary of aggregate characteristics.

a, Histograms displaying the distribution of cell counts per aggregate for AS and AD consortia, blue and green respectively. b, Histograms displaying the average activity values for the AS and AD consortia, where anabolic activity is measured as fractional abundance of 15N per cell. c, Histograms of the number of AS and AD consortia associated with different levels of spatial mixing between syntrophic partners represented by the spatial mixing metric ‘J’ (see Supplementary Discussion for details on this metric). d, One-to-one relation between bacterial and archaeal cell counts in the AS and AD consortia analysed in this study. For all panels, the data set consists of 41 AS and 21 AD consortia. The number of cells in each aggregate can be found in the Source Data.

Source data

Extended Data Figure 4 Illustration of the value of single-cell resolution activity analysis.

a, Box plots showing the full range of archaeal and bacterial single-cell activities determined by 15NH4+ assimilation. The difference between the archaeal and bacterial mean activities across all aggregates (n = 62) is not significant (two sample _t_-test, P > 0.05). b, With our ability to quantify the activity for individual phylogenetically identified cells in AOM consortia, the average activity of the bacterial and archaeal populations within each consortium was revealed. Assessed at the level of paired populations, a significant difference in activity between the population of archaea and Deltaproteobacteria within aggregates is evident (n = 62, paired-sample _t_-test, P < 0.001). c**, d, Adding phylogenetic resolution to this analysis by sub-grouping consortia based on their different deltaproteobacterial partners (AD and AS) reveals the difference between bacteria and archaea is only significant in the AS consortia (n = 41, paired-sample _t_-test, P < 0.001), while this population level offset in activity was not statistically supported within the AD group (_n_ = 21, paired-sample _t_-test, _P_ > 0.05), illustrating differential patterns in activity related to species membership. All axes represent 15N fractional abundance. The 8 consortia images shown in panels b–d** represent a subset of the total 62 consortia included in the analysis, with each image coloured by either archaeal 15N enrichment on the left (green) or bacterial 15N enrichment on the right (pink). The degree of brightness for each cell in the image reflects increasing levels of relative cellular 15N enrichment and the average population value for 15N fractional abundance is provided on the central axis.

Source data

Extended Data Figure 5 Evaluation of metrics for partner mixing.

The degree of partner intermixing within an aggregate was calculated using two metrics (see Supplementary Information for detailed description of metrics). For the modified join metric (J), 1 represents random mixing, while for Moran’s I, 0 represents random mixing. For both metrics increasing positive values represent increasing partner segregation and increasing negative values represent increasing ordered mixing (like a checkerboard). a, Examples of mock aggregates which were used to verify the behaviour of the two metrics. b, c, The determined values for either J or Moran’s I are represented by the large coloured data points for each of the 41 AS aggregates or 21 AD aggregates analysed in this study, respectively. The black data points represent the values for J or Moran’s I that were calculated in 300 permutation tests where the x and y coordinates of the archaea and bacteria cells were randomly reassigned. When the observed mixing was more segregated than 95% of the random permutation tests, the data points were coloured green and considered significant. Similarly, when the observed mixing was found to be more orderly mixed than 95% of the permutation tests the data points were coloured purple. When the observed mixing was found to be less extreme in either direction than 95% of the random test aggregates the data points were coloured red. The two metrics, while different in their formulation, gave very similar results. It is noteworthy that only a single aggregate contained cells that were more mixed than random. As expected, the permutation tests hover around the random mixing values for each metric, 1 and 0 for J and I, respectively.

Extended Data Figure 6 Insensitivity of cell activities to distance from nearest syntrophic partner for AD consortia.

Plots displaying all ROIs analysed of a given type for consortia composed of ANME-2b or ANME-2c and Deltaproteobacteria. Normalized activity (_Z_-scores) were calculated within each aggregate to allow for comparisons between consortia with large differences in average cellular activity. a, Normalized activities of archaea (n = 765 cells) within AD consortia as a function of distance to nearest syntrophic partner. b, Normalized activities of bacteria (n = 658 cells) within AD consortia as a function of distance to nearest syntrophic partner. From this analysis, it appears that distance to nearest syntrophic partner does not account for a significant amount of the variation in cellular activity within a consortium. The _R_2 values for linear regressions on the plotted data are shown in each panel. Dashed lines illustrate the 95% confidence intervals in slopes and intercepts of the linear regressions.

Source data

Extended Data Figure 7 Schematic of network analysis for microbial consortia.

a, FISH image of a representative ANME (green) and SRB (pink) consortium. b, Highlighted regions of interest false coloured by phylogenetic affiliation. c, Spheres of influence network of the consortia showing connectivity between cells. d, Identification of cells that share a border with a syntrophic partner (archaea adjacent to bacteria).

Extended Data Figure 8 Insensitivity of cell activities to distance from surface.

Plots displaying all ROIs analysed for a given population. Normalized activities (_Z_-scores) were taken within each consortium to allow for comparisons between aggregates with large differences in average cellular activity. a, Normalized activities of archaea within AS aggregates (n = 1,967 cells) as a function of distance to aggregate surface (that is, the external environment). b, Normalized activities of bacteria (n = 2,063 cells) within AS aggregates as a function of distance to aggregate surface. c, Normalized activities of archaea (n = 765 cells) within AD aggregates as a function of distance to aggregate surface. d, Normalized activities of bacteria (n = 658 cells) within AD aggregates as a function of distance to aggregate surface. From this analysis, the distance to the surface of the aggregate does not appear to explain a significant amount of the variation in cellular activity within each consortium. The _R_2 values for linear regressions on the plotted data are shown in each panel. Dashed lines illustrate the 95% confidence intervals in slopes and intercepts of the linear regressions.

Source data

Extended Data Figure 9 Spatial and geometric relationships for all modelled aggregate geometries as a function of relative conductivity within the direct electron transfer model.

a, Total aggregate activity normalized to the group maximum as a function of the J spatial metric, from well-mixed (low J) to segregated (high J) aggregate geometries (23 in silico aggregates in total). These plots illustrate how the total activity of all of aggregate geometries changes with the relative conductivity, with less dependency on geometry observed at the fastest conductance rates. Compare to Extended Data Fig. 2: in the case of electron exchange presented here, the least mixed aggregates (high J) have the highest activity. This is because our conductive treatment of the aggregate relies on the global electric potential of each consortia, which is the strongest when the cells are spatially organized. b, Normalized archaeal activity plotted against the normalized bacterial activity within the same modelled aggregate. c, The normalized (_z_-score) activity for archaea (green) and bacteria (red) plotted against the distance to the nearest three partners. d, The _z_-score activity for archaea (green) and bacteria (red) plotted against the distance to environment-aggregate interface (aggregate surface). In plots c and d the _r_-squared values for each correlation are given at the top of each plot in colours that correspond to the two cell types. The number of modelled in silico bacterial and archaeal cells from c and d plotted in the columns from left to right are: 1,138 bacterial and 1,162 archaeal cells; 1,161 bacterial cells and 1,139 archaeal cells; and 1,134 bacterial and 1,166 archaeal cells.

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McGlynn, S., Chadwick, G., Kempes, C. et al. Single cell activity reveals direct electron transfer in methanotrophic consortia.Nature 526, 531–535 (2015). https://doi.org/10.1038/nature15512

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