The marine deep biosphere is the largest microbial habitat on Earth, and a 2022 study of the Scotian Slope (NW Atlantic) proposed that geological processes operate a 'microbial dispersal loop': thermophilic endospores (dormant, heat-resistant resting stages of heat-loving bacteria) are transported upward from deep petroleum systems by hydrocarbon seepage, dispersed through the ocean, re-buried by sedimentation, and can eventually germinate when burial returns them to warm, petroleum-bearing depths. The loop's global prevalence, the actual timescales of upward transport and burial, its quantitative contribution to maintaining deep biosphere biomass, and the direct reactivation and growth of buried endospores in newly forming petroleum systems all remain unresolved. This problem asks whether the loop is a quantitatively significant, globally operating mechanism that maintains deep biosphere standing biomass, or a locally documented curiosity.

Background

The deep biosphere — the microbial habitat in marine sediments and crust below the seabed — is the largest microbial habitat on Earth, holding on the order of 102910^{29} cells and a substantial fraction of all microbial biomass. Its populations survive at extraordinarily low energy fluxes, and how this standing biomass is maintained over geological time is a central question of deep-subsurface ecology. Bacterial endospores are dormant, extremely resistant resting stages formed by certain bacteria (chiefly the phylum Firmicutes, reclassified as Bacillota); their abundance is tracked by the biomarker dipicolinic acid (DPA), a small molecule that makes up a large fixed fraction of endospore dry weight. 'Thermospores' are endospores of thermophilic (heat-loving) bacteria that are routinely found in permanently cold marine surface sediments worldwide, far from any environment warm enough for their growth. They are thought to be expelled from warm subsurface habitats and dispersed by ocean currents: thermospores buried in Baltic Sea sediments over thousands of years remain viable (de Rezende et al. 2013), and in the deep Gulf of Mexico thermospore abundance correlates with migrated thermogenic hydrocarbons (oil and gas formed by burial heating of organic-rich source rocks and rising from depth), implicating seepage from deep oil reservoirs as the dispersal vector (Chakraborty et al. 2018). Globally, endospores outnumber vegetative cells below about 25 m below seafloor, with an estimated 2.5×10282.5\times10^{28} to 1.9×10291.9\times10^{29} endospores in the uppermost kilometer of sediment (Wörmer et al. 2019), but whether low-frequency germination of this seed bank materially sustains deep populations is unresolved.

A petroleum system is a subsurface domain where organic-rich source rocks generate and expel oil and gas into reservoir rocks; 'newly forming' petroleum systems are burial horizons just entering the temperature window where petroleum generation and thermophilic germination (above roughly 40 ∘C40\,^{\circ}\mathrm{C}) both become possible. Combining seismic reflection imaging (which maps deep faults and hydrocarbon indicators), seafloor geochemistry, DPA quantification, high-temperature germination incubations, and metagenomics, Gittins et al. (2022) showed on the Scotian Slope offshore Nova Scotia that thermophilic endospores in cold seabed sediments sit directly above seep conduits rooted in petroleum-bearing sediments ~2 km below the seafloor, carry genomes adapted to anoxic hydrocarbon degradation, and closely resemble oil-reservoir microbiomes from around the world. Viable thermospores occur throughout the top several meters of seabed and are constantly re-buried at an estimated ~10810^{8} spores m−2^{-2} year−1^{-1} (Gittins et al. 2022). Together these observations define a closed 'subsurface microbial loop': upward seep transport of dormant cells, lateral ocean dispersal, sedimentary re-burial, and eventual germination and selection where burial warms them into newly forming petroleum systems. However, the published timescale estimates — tens to hundreds of years for upward transport at seepage rates of ~10 cm day−1^{-1}, and on the order of 10710^{7} years for burial descent to >40 ∘C>40\,^{\circ}\mathrm{C} horizons — are explicitly order-of-magnitude inferences, not measurements, and the study examined a single margin. Follow-up work has only sharpened the gap: further Scotian Slope cores corroborate the endospore–seep association regionally (Rattray et al. 2023), whereas Laptev Sea shelf sediments show spatially restricted thermospore distributions suggesting geofluid dispersal there is limited (Ståhl et al. 2024); laboratory incubations confirm thermospores can germinate and metabolize at 80 ∘C80\,^{\circ}\mathrm{C} (Bell et al. 2020, 2022), but no in-situ reactivation in a newly forming petroleum system has been observed; and oil-reservoir microbiome surveys show environmental selection shapes reservoir communities without core cosmopolitan taxa (Gittins et al. 2023). Deep-sourced cold seeps are now documented being maintained by deep biosphere 'oases' on the same margin (Chowdhury et al. 2024), yet nothing quantifies how much the loop contributes to maintaining the deep biosphere's biomass.

Problem Statement

Determine the global prevalence and quantitative significance of the geologically mediated subsurface microbial dispersal loop — upward seepage transport of thermophilic endospores from deep petroleum systems, oceanic dispersal, sedimentary re-burial, and eventual germination and selection in warm subsurface horizons — as a mechanism maintaining deep biosphere biomass. Concretely: (1) establish, through comparable multi-margin investigation of settings where hydrocarbon seepage and sedimentation are coupled, how geographically widespread and how uniformly intense this loop operates, relative to the Scotian Slope type example; (2) constrain the actual timescales of the upward transport and burial legs, replacing the current order-of-magnitude inferences (tens to hundreds of years upward at ~10 cm day−1^{-1} seepage; ~10710^{7} years of burial descent to >40 ∘C>40\,^{\circ}\mathrm{C} horizons) with measured or tightly bounded values; (3) quantify the loop's contribution to the deep biosphere biomass budget — e.g., whether loop-supplied germination and population replenishment fluxes (∼108\sim10^{8} spores m−2^{-2} year−1^{-1} buried at the Scotian Slope) are a first-order term relative to maintenance and death rates of indigenous deep communities; and (4) directly test the proposed completion of the loop by investigating reactivation and growth of buried endospores in newly forming petroleum systems, either in situ or under verified in-situ conditions. The overarching objective uniting these components is to decide whether this loop is a quantitatively significant, globally operating mechanism of deep biosphere maintenance, or a locally documented process of minor global significance. A complete resolution must address all four components; each is required, and answering only a subset (or only the overarching verdict) does not resolve the task. The verdict is the joint outcome of two independently established dimensions — the loop's geographic extent and uniformity of intensity (component 1) and its contribution to the deep biosphere biomass budget (component 3) — so that a loop which proves globally widespread yet quantitatively minor, or locally intense, is resolved by reporting both dimensions rather than by fitting into either label alone.

References

  1. Gittins DA, Desiage P-A, Morrison N, Rattray JE, Bhatnagar S, Chakraborty A, Zorz J, Li C, Horanszky O, Cramm MA, Bisiach F, Bennett R, Webb J, MacDonald A, Fowler M, Campbell DC, Hubert CRJ (2022) 'Geological processes mediate a microbial dispersal loop in the deep biosphere', Science Advances 8(34), eabn3485. DOI: 10.1126/sciadv.abn3485. https://doi.org/10.1126/sciadv.abn3485
  2. Gittins DA, Desiage P, Morrison N, Rattray JE, Bhatnagar S, Chakraborty A, Zorz J, Li C, Horanszky O, Cramm MA, Webb J, MacDonald A, Fowler M, Campbell DC, Hubert CRJ (2021) 'Geological processes mediate a subsurface microbial loop in the deep biosphere', bioRxiv preprint. DOI: 10.1101/2021.10.26.465990. https://doi.org/10.1101/2021.10.26.465990
  3. Wörmer L, Hoshino T, Bowles MW, Viehweger B, Adhikari RR, Xiao N, Uramoto G, Könneke M, Lazar CS, Morono Y, Inagaki F, Hinrichs K-U (2019) 'Microbial dormancy in the marine subsurface: Global endospore abundance and response to burial', Science Advances 5(2), eaav1024. DOI: 10.1126/sciadv.aav1024. https://doi.org/10.1126/sciadv.aav1024
  4. de Rezende JR, Kjeldsen KU, Hubert CRJ, Finster K, Loy A, Jørgensen BB (2013) 'Dispersal of thermophilic Desulfotomaculum endospores into Baltic Sea sediments over thousands of years', The ISME Journal 7(1), 72–84. DOI: 10.1038/ismej.2012.83. https://doi.org/10.1038/ismej.2012.83
  5. Chakraborty A, Ellefson E, Li C, Gittins D, Brooks JM, Bernard BB, Hubert CRJ (2018) 'Thermophilic endospores associated with migrated thermogenic hydrocarbons in deep Gulf of Mexico marine sediments', The ISME Journal 12(8), 1895–1906. DOI: 10.1038/s41396-018-0108-y. https://doi.org/10.1038/s41396-018-0108-y
  6. Bell E, Rattray JE, Sloan K, Sherry A, Pilloni G, Hubert CRJ (2022) 'Hyperthermophilic endospores germinate and metabolize organic carbon in sediments heated to 80°C', Environmental Microbiology 24(11), 5534–5545. DOI: 10.1111/1462-2920.16167. https://doi.org/10.1111/1462-2920.16167
  7. Bell E, Sherry A, Pilloni G, Suárez-Suárez A, Cramm MA, Cueto G, Head IM, Hubert CRJ (2020) 'Sediment cooling triggers germination and sulfate reduction by heat-resistant thermophilic spore-forming bacteria', Environmental Microbiology 22(1), 456–465. DOI: 10.1111/1462-2920.14866. https://doi.org/10.1111/1462-2920.14866
  8. Rattray JE, Elizondo G, Sloan K, Morrison N, Fowler M, Gittins DA, Webb J, Campbell DC, MacDonald A, Hubert CRJ (2023) 'Elevated bacterial endospores associated with thermogenic hydrocarbon seeps in deep sea sediments', Organic Geochemistry 177, 104568. DOI: 10.1016/j.orggeochem.2023.104568. https://doi.org/10.1016/j.orggeochem.2023.104568
  9. Ståhl E, Linderholm A, Brüchert V (2024) 'A Spatially Restricted Distribution of Thermophilic Endospores in Laptev Sea Shelf Sediments Suggests a Limited Dispersal by Local Geofluids', Geobiology 22(5), e12618. DOI: 10.1111/gbi.12618. https://doi.org/10.1111/gbi.12618
  10. Chowdhury A, Ventura GT, Owino Y, Lalk EJ, MacAdam N, Dooma JM, Ono S, Fowler M, MacDonald A, Bennett R, MacRae RA, Hubert CRJ, Bentley JN, Kerr MJ (2024) 'Cold seep formation from salt diapir–controlled deep biosphere oases', Proceedings of the National Academy of Sciences USA 121(12), e2316878121. DOI: 10.1073/pnas.2316878121. https://doi.org/10.1073/pnas.2316878121
  11. Gittins DA, Bhatnagar S, Hubert CRJ (2023) 'Environmental Selection and Biogeography Shape the Microbiome of Subsurface Petroleum Reservoirs', mSystems 8(2), e00884-22. DOI: 10.1128/msystems.00884-22. https://doi.org/10.1128/msystems.00884-22