Iron-oxidizer hotspots formed by intermittent oxic–anoxic fluid mixing in fractured rocks


Subsurface environments host most of the fresh water on Earth as well as diverse microorganisms that may constitute a significant part of the biosphere. However, the dynamics and spatial distribution of subsurface microorganisms and their response to hydrological processes are poorly understood. Here we used chemical and metagenomic analyses of groundwater in a fractured rock aquifer in western France to determine the role of fractures in the formation of deep microbial hotspots in the subsurface. The majority of fractures, sampled in a 130-m-deep borehole, were anoxic, but a fracture carrying oxic groundwater was detected at 54-m depth, associated with a fivefold increase in the abundance of iron-oxidizing bacteria. We developed a mechanistic model of fluid flow and mixing in fractures and found that such microbial hotspots are sustained by the mixing of fluids with contrasting redox chemistries at intersections of fractures. The model predicts that metre-scale changes in near-surface water table levels cause intermittent oxygen delivery through deep fractures, which can extend the depth of the habitable zone for iron-oxidizing bacteria hundreds of metres into the subsurface. Given that fractures are ubiquitous at multiple scales in the subsurface, such deep microbial hotspots may substantially influence microbial communities and their effect on Earth’s biogeochemical cycles.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Flow patterns, redox gradients and reactive mixing hotspots in the subsurface.
Fig. 2: Fracture distribution, density, orientations, flow rates and chemical properties in borehole PZ26.
Fig. 3: Biomineral filaments formed by FeOB and metagenome-based relative abundance of Gallionellaceae in fracture fluids at different depths.
Fig. 4: Depth and temporal fluctuations of the simulated habitable zone for FeOB at fracture intersections.

Data availability

The data that support the findings of this study were measured at the Ploemeur fractured rock observatory, belonging to the French network of hydrogeological sites H+ ( They are available from the H+ database:

Code availability

The Matlab code developed to simulate the depth of the habitable zone for FeOB (Fig. 4) is available at


  1. 1.

    Maher, K. & Chamberlain, C. Hydrologic regulation of chemical weathering and the geologic carbon cycle. Science 343, 1502–1504 (2014).

  2. 2.

    Li, L. et al. Expanding the role of reactive transport models in critical zone processes. Earth Sci. Rev. 165, 280–301 (2017).

  3. 3.

    Battin, T. J., Besemer, K., Bengtsson, M. M., Romani, A. M. & Packmann, A. I. The ecology and biogeochemistry of stream biofilms. Nat. Rev. Microbiol. 14, 251–263 (2016).

  4. 4.

    McMahon, P. Aquifer/aquitard interfaces: mixing zones that enhance biogeochemical reactions. Hydrogeol. J. 9, 34–43 (2001).

  5. 5.

    McClain, M. et al. Biogeochemical hot spots and hot moments at the interface of terrestrial and aquatic ecosystems. Ecosystems 6, 301–312 (2003).

  6. 6.

    Frei, S., Knorr, K. H., Peiffer, S. & Fleckenstein, J. H. Surface micro-topography causes hot spots of biogeochemical activity in wetland systems: a virtual modeling experiment. J. Geophys. Res. 117, G00N12 (2012).

  7. 7.

    Cardenas, M. B. Hyporheic zone hydrologic science: a historical account of its emergence and a prospectus. Water Resour. Res. 51, 3601–3616 (2015).

  8. 8.

    Bernhardt, E. S. et al. Control points in ecosystems: moving beyond the hot spot hot moment concept. Ecosystems 20, 665–682 (2017).

  9. 9.

    Kallmeyer, J. & Wagner, D. Microbial Life of the Deep Biosphere (De Gruyter, 2014).

  10. 10.

    Chapelle, F. Ground-Water Microbiology and Geochemistry (John Wiley and Sons, 2001).

  11. 11.

    Brune, A., Frenzel, P. & Cypionka, H. Life at the oxic anoxic interface: microbial activities and adaptations. FEMS Microbiol. Rev. 24, 691–710 (2000).

  12. 12.

    Boano, F. et al. Hyporheic flow and transport processes: mechanisms, models, and biogeochemical implications. Rev. Geophys. 52, 603679 (2014).

  13. 13.

    Stegen, J. C. et al. Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover. Nat. Commun. 7, 11237 (2015).

  14. 14.

    Long, P., Williams, K., Hubbard, S. & Banfield, J. Microbial metagenomics reveals climate-relevant subsurface biogeochemical processes. Trends Microbiol. 24, 600–610 (2016).

  15. 15.

    Pedersen, K. Microbial life in deep granitic rock. FEMS Microbiol. Rev. 20, 399–414 (1997).

  16. 16.

    Breuker, A., Köweker, G., Blazejak, A. & Schippers, A. The deep biosphere in terrestrial sediments in the Chesapeake Bay area, Virginia, USA. Front. Microbiol. 2, 1–13 (2011).

  17. 17.

    Nyyssönen, M. et al. Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield. ISME J. 8, 126–138 (2014).

  18. 18.

    Santelli, C. M. et al. Abundance and diversity of microbial life in ocean crust. Nature 453, 653–656 (2008).

  19. 19.

    Ménez, B., Pasini, V. & Brunelli, D. Life in the hydrated suboceanic mantle. Nat. Geosci. 5, 133–137 (2012).

  20. 20.

    Trias, R. et al. High reactivity of deep biota under anthropogenic CO2 injection into basalt. Nat. Commun. 8, 1063 (2017).

  21. 21.

    Kolbe, T. et al. Stratification of reactivity determines nitrate removal in groundwater. Proc. Natl Acad. Sci. USA 116, 2494–2499 (2019).

  22. 22.

    Edwards, K. J., Becker, K. & Colwell, F. The deep, dark energy biosphere: intraterrestrial life on Earth. Annu. Rev. Earth Planet. Sci. 40, 551–568 (2012).

  23. 23.

    Alain, K. et al. Microbial Life of the Deep Biosphere Vol. 1 (Walter de Gruyter, 2014).

  24. 24.

    Bonnet, E. et al. Scaling of fracture systems in geological media. Rev. Geophys. 39, 347–383 (2001).

  25. 25.

    St Clair, J. et al. Geophysical imaging reveals topographic stress control of bedrock weathering. Science 350, 534–538 (2015).

  26. 26.

    Martinez-Landa, L. et al. Mixing induced reactive transport in fractured crystalline rocks. Appl. Geochem. 27, 479–489 (2012).

  27. 27.

    Melton, E. D., Swanner, E., Behrens, S., Schmidt, C. & Kappler, A. The interplay of microbially mediated reactions in the biogeochemical Fe cycle. Nat. Rev. Microbiol. 12, 797–808 (2014).

  28. 28.

    Anderson, C. R. & Pedersen, K. In situ growth of Gallionella biofilms and partitioning of lanthanides and actinides between biological material and ferric oxyhydroxides. Geobiology 1, 169–178 (2003).

  29. 29.

    Quaiser, A. et al. Unraveling the stratification of an iron-oxidizing microbial mat by metatranscriptomics. PLoS ONE 9, 1–9 (2014).

  30. 30.

    Fleming, E. J., Cetinić, I., Chan, C. S., King, D. W. & Emerson, D. Ecological succession among iron-oxidizing bacteria. ISME J. 8, 804–815 (2014).

  31. 31.

    McAllister, S. M. et al. Dynamic hydrologic and biogeochemical processes drive microbially enhanced iron and sulfur cycling within the intertidal mixing zone of a beach aquifer. Limnol. Oceanogr. 60, 329–345 (2015).

  32. 32.

    Revsbech, D. & Emerson, N. P. Investigation of an iron-oxidizing microbial mat community located near Aarhus, Denmark: field studies. Appl. Environ. Microbiol. 60, 4022–4031 (1994).

  33. 33.

    Emerson, D. & Moyer, C. L. Neutrophilic Fe-oxidizing bacteria are abundant at the Loihi Seamount hydrothermal vents and play a major role in Fe oxide deposition. Appl. Environ. Microbiol. 68, 3085–3093 (2002).

  34. 34.

    Ben Maamar, S. et al. Groundwater isolation governs chemistry and microbial community structure along hydrologic flowpaths. Front. Microbiol. 6, 1–13 (2015).

  35. 35.

    Bach, W. & Edwards, K. J. Iron and sulfide oxidation within the basaltic ocean crust: implications for chemolithoautotrophic microbial biomass production. Geochim. Cosmochim. Acta 67, 3871–3887 (2003).

  36. 36.

    Emerson, D. et al. Comparative genomics of freshwater Fe-oxidizing bacteria: implications for physiology, ecology, and systematics. Front. Microbiol. 4, 1–17 (2013).

  37. 37.

    Kato, S. et al. Comparative genomic insights into ecophysiology of neutrophilic, microaerophilic iron oxidizing bacteria. Front. Microbiol. 6, 1–16 (2015).

  38. 38.

    LeBorgne, T., Bour, O., Paillet, F. L. & Caudal, J. P. Assessment of preferential flow path connectivity and hydraulic properties at single-borehole and cross-borehole scales in a fractured aquifer. J. Hydrol. 328, 347–359 (2006).

  39. 39.

    Dorn, C., Linde, N., LeBorgne, T., Bour, O. & Baron, L. Single-hole GPR reflection imaging of solute transport in a granitic aquifer. Geophys. Res. Lett. 38, L08401 (2011).

  40. 40.

    Purkamo, L. et al. Dissecting the deep biosphere: retrieving authentic microbial communities from packer-isolated deep crystalline bedrock fracture zones. FEMS Microbiol. Ecol. 85, 324–337 (2013).

  41. 41.

    Sorensen, J. P. R. et al. Using boreholes as windows into groundwater ecosystems. PLoS ONE 8, e70264 (2013).

  42. 42.

    Ayraud, V. et al. Compartmentalization of physical and chemical properties in hard-rock aquifers deduced from chemical and groundwater age analyses. Appl. Geochem. 23, 2686–2707 (2008).

  43. 43.

    Hallbeck, L., Stahl, F. & Pedersen, K. Phylogeny and phenotypic characterization of the stalk-forming and iron-oxidizing bacterium Gallionella ferruginea. J. Gen. Microbiol. 139, 1531–1535 (1993).

  44. 44.

    Kato, S., Krepski, S., Chan, C., Itoh, T. & Ohkuma, M. Ferriphaselus amnicola gen. nov., sp. nov., a neutrophilic, stalk-forming, iron-oxidizing bacterium isolated from an iron-rich groundwater seep. Int. J. Syst. Evol. Microbiol. 64, 921–925 (2014).

  45. 45.

    Castelle, C. J. et al. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat. Commun. 4, 2120 (2013).

  46. 46.

    Jimenez-Martinez, J. et al. Temporal and spatial scaling of hydraulic response to recharge in fractured aquifers: insights from a frequency domain analysis. Water Resour. Res. 49, 3007–3023 (2013).

  47. 47.

    Druschel, G. K., Emerson, D., Sutka, R., Suchecki, P. & Luther, G. W. Low-oxygen and chemical kinetic constraints on the geochemical niche of neutrophilic iron(II) oxidizing microorganisms. Geochim. Cosmochim. Acta 72, 3358–3370 (2008).

  48. 48.

    Gleeson, T., Befus, K. M., Jasechko, S., Luijendijk, E. & Cardenas, M. B. The global volume and distribution of modern groundwater. Nat. Geosci. 9, 161–167 (2016).

  49. 49.

    Kang, P. K., LeBorgne, T., Dentz, M., Bour, O. & Juanes, R. Impact of velocity correlation and distribution on transport in fractured media: field evidence and theoretical model. Water Resour. Res. 51, 940–959 (2015).

  50. 50.

    Shakas, A. et al. Hydrogeophysical characterization of transport processes in fractured rock by combining push–pull and single-hole ground penetrating radar experiments. Water Resour. Res. 52, 938–953 (2016).

  51. 51.

    Ruelleu, S., Moreau, F., Bour, O., Gapais, D. & Martelet, G. Impact of gently dipping discontinuities on basement aquifer recharge: an example from Ploemeur (Brittany, France). J. Appl. Geophys. 70, 161–168 (2010).

  52. 52.

    Klepikova, M. V., LeBorgne, T., Bour, O. & Davy, P. A methodology for using borehole temperature-depth profiles under ambient, single and cross-borehole pumping conditions to estimate fracture hydraulic properties. J. Hydrology 407, 145–152 (2011).

  53. 53.

    Paillet, F. L. A field technique for estimating aquifer parameters using flow log data. Groundwater 38, 510–521 (2000).

  54. 54.

    Berkowitz, B. Characterizing flow and transport in fractured geological media: a review. Adv. Water Resour. 25, 861–884 (2002).

  55. 55.

    Witherspoon, P. A., Wang, J. S., Iwai, K. & Gale, J. E. Validity of cubic law for fluid flow in a deformable rock fracture. Water Resour. Res. 16, 1016–1024 (1980).

  56. 56.

    Emerson, D., Fleming, E. J. & McBeth, J. M. Iron-oxidizing bacteria: an environmental and genomic perspective. Annu. Rev. Microbiol. 64, 561–583 (2010).

  57. 57.

    Menzel, P., Ng, K. L. & Krogh, A. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat. Commun. 7, 11257 (2016).

Download references


Funding was provided by the ERC project ReactiveFronts (648377), the ANR projects CRITEX (ANR-11-EQPX-0011), Subsurface mixing and reactions (ANR-14-CE04-0003) and Stock-en-Socle (ANR-13-SEED-0009), ADEME and Région Bretagne. We thank the Ploemeur observatory (H+ network and OZCAR Network of Critical Zone Observatories) for providing data and field support for this study. We thank L. Longuevergne and O. Bour, respectively principal investigators of the Ploemeur site and of the H+ network, for providing access to the site and to the data, and support for the organization of field campaigns. We thank M. Bouhnik-Le-Coz and P. Petitjean for chemical analysis, CMEBA for SEM imaging, CONDATE EAU for dissolved gas analysis, M. Chorin for light and fluorescence microscopy, A. Quaiser, S. Michon-Coudouel and M. Biget for metagenome sequencing and S. Gu for the Chinese translation of the abstract. We finally thank Y. Duclos, S. Ben Maamar, T. Babey, G. Baby and P. Davy for their help and stimulating scientific discussions.

Author information

O.B. led the field campaigns, batch tests, data interpretation, model development and results formatting. L.B. carried out metagenome production and draft genome assembly. A.D. supervised metagenomic data analysis and interpretation. J.F. managed bacteria sampling and characterization in field campaigns and batch experiments, and performed hydrochemical borehole logging. M.P. performed chemical and SEM analysis of fluids and microbial mat sampled in field campaigns and batch experiments. T.L. and E.C. managed measurements of dissolved gases and CFC in field campaigns. N.L. developed the packer system and managed borehole flow and pressure measurements. C.P. handled logistics related to field campaigns. B.W.A. contributed to formalize biogeochemical implications of results, manuscript editing and proofreading. L.A. supervised geochemical and metagenomic data interpretation. T.L.B. designed the research and supervised data interpretation, modelling and manuscript writing.

Correspondence to Tanguy Le Borgne.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information Primary Handling Editor: Rebecca Neely.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Distribution of oxygen and flow patterns at the study site.

a. Map of borehole locations and oxygen distribution at 20 meters depth interpolated from borehole oxygen profiles (Extended Data Fig. 2b). b. Conceptual model of oxic and anoxic flow in the subsurface. Oxic boreholes (PZ15, PZ21, PSR1 and PSR2) are located on high topographic areas, where the near surface piezometric level is higher than the deep piezometric level (recharges areas). This induces downward flow of oxygen in permeable fractures. Anoxic boreholes (PZ2, PZ19, PZ22, PZ23, PZ24, PZ25, PZ26, PSR5) are located in low topographic areas, where the deep piezometric levels are higher than near surface piezometric levels (discharge areas). This induces upward flow of reduced water up to the surface. As these fluxes occur through a complex fracture network, this leads to mixing of oxic and anoxic fluids at fracture intersections (yellow dots).

Extended Data Fig. 2 Piezometric levels and oxygen profiles.

a. Evolution of piezometric levels over time for two boreholes located respectively in recharge (PZ15) and discharge (PZ23) areas. b. Oxygen concentration profiles with depth in the 12 boreholes. The boreholes representative of recharge areas are represented in shades of blue colors, while those representative of discharge areas are represented in shades of red colors. A model of average oxygen concentration decay by biogeochemical activity (equation (4)) is fitted from the oxygen evolution with depth observed in the deepest boreholes representative of recharge areas, PSR1 and PSR2 (dashed black line).

Extended Data Fig. 3 Intermittent oxygen delivery in the subsurface in response to water table change during a hydrological year.

a. Evolution of the piezometric levels during the hydrological year 2016/2017 in boreholes representative respectively of the recharge areas (PZ15, blue line) and of the deep fractured zone (PZ23, orange line) in response to the cumulative rainfall (grey histogram). b. Temperature (left) and oxygen (right) profiles at two different times, representative of the recharge period (13/04/2017, blue lines) and of the dry period (20/10/2017, red lines).

Extended Data Fig. 4 Optical logs and video images of borehole PZ26.

a. Snapshots of \(36{0}^{\circ }\) optical logs showing the main permeable fractures. The dark regions correspond to open fractures. Small fractures composing F37 and F59 are highlighted in red. The vertical and horizontal scales are indicated at the bottom left. b. Location and relative transmissivity of the main permeable fractures. c. Snapshots of borehole video showing an example location where the microbial mat is clogging the borehole (30 m), the oxic fracture F54 (53.6 m), an example of non fractured zone (68.6 m) and a deep reduced fracture (73.6 m), see also Supplementary Video.

Extended Data Fig. 5 Sampling of fracture fluid in borehole PZ26.

a. Natural discharge from the deep fractures towards the surface in the PZ26 artesian borehole. All fractures are under pressure and constantly produce flow towards the top of the borehole. Therefore, dissolved oxygen cannot diffuse from the surface through the borehole and any oxygen molecule contributing to iron oxidation has to be transported through the fracture network. b. Field sampling of pristine fracture fluid in borehole PZ26 with a packer. c. Sketch of the packer sampling method. In this example, the targeted fracture is F37. The large pump at the top of the well draws water from all fractures above the packer. Hence the small pump in front of F37 only pumps water from F37. The packer prevents any flow from fractures located below it.

Extended Data Fig. 6 Batch experiments for monitoring the kinetics of iron oxidation and oxygen consumption during mat formation.

a. Formation of the microbial mat in the sampling bottles. b. Evolution of dissolved oxygen (blue) and iron (orange) concentration, pH (green), and redox potential (purple) as a function of time.

Extended Data Fig. 7 Estimated depths, hydraulic properties, apertures and sampling radii of the permeable fractures in borehole PZ26.

The depth of permeable fracture is estimated from the flow and optical logs (Fig. 2). Relative and absolute fractures transmissivities are estimated from equation (1) with \({T}_{tot}=5.1{0}^{-3}\,{\rm{m}}^{2}\,.{\rm{s}}^{-1}\). The fracture aperture is estimated by inverting equation (2) with \(\rho =1{0}^{3}\,{\rm{kg}}/{\rm{m}}^{3}\), \(g = 9.81\,{\rm{m}}/{\rm{s}}^{2}\) and \(\mu = 1.1410^{-3}\,{\rm{kg}}/{\rm{m}}/{\rm{s}}\). The sampling radius is estimated from equation (3).

Extended Data Fig. 8

Iron speciation in each sampled zone.

Supplementary information


A borehole video (.avi format) showing the distribution of the FeOB microbial mat in borehole PZ26. The video shows selected sections of the borehole up to 84-m depth.

The same as Video 1 in .mov format.

Supplementary Information

Details of the model derivation and metagenomic analysis, Figs. 1–5 and Tables 1–3.

Supplementary Video 1

A borehole video (.avi format) showing the distribution of the FeOB microbial mat in borehole PZ26. The video shows selected sections of the borehole up to 84-m depth.

Supplementary Video 2

The same as Video 1 in .mov format.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Bochet, O., Bethencourt, L., Dufresne, A. et al. Iron-oxidizer hotspots formed by intermittent oxic–anoxic fluid mixing in fractured rocks. Nat. Geosci. 13, 149–155 (2020).

Download citation