pith. sign in

arxiv: 2604.07768 · v1 · submitted 2026-04-09 · ⚛️ physics.bio-ph · cond-mat.mtrl-sci· cond-mat.soft· physics.flu-dyn· physics.geo-ph

Biogenic bubbles enable microbial escape from physical confinement

Babak Vajdi Hokmabad , Thomas Appleford , Hao Nghi Luu , Meera Ramaswamy , Maziyar Jalaal , Sujit S. Datta This is my paper

Pith reviewed 2026-05-10 18:24 UTC · model grok-4.3

classification ⚛️ physics.bio-ph cond-mat.mtrl-scicond-mat.softphysics.flu-dynphysics.geo-ph
keywords microbial dispersalbiogenic bubblesyield stress fluidsfermentationactive matterphysical confinementyeast
0
0 comments X

The pith

Immotile microbes disperse long-range in confining matrices by producing and riding biogenic bubbles from their metabolism.

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

Immotile microbes like yeast are trapped in many natural environments, yet they need to disperse. This paper shows they use their own fermentation to create CO2 bubbles that break through the confining material and carry cells upward as the bubbles rise. These bubbles form repeatedly, building tall columns of colonies that extend much farther than growth would allow alone. Colonies can even connect and share cells through the networks they create together. This uncovers a new way microbes move without swimming or just growing, by changing their physical surroundings with metabolic byproducts.

Core claim

Immotile microbial colonies confined in a model transparent yield-stress matrix can achieve long-range dispersal by harnessing their own metabolism. Fermentation drives dissolved CO2 to supersaturation, nucleating biogenic bubbles that grow, yield the matrix, and rise, hydrodynamically entraining cells vertically in their wake. Sequential bubble nucleation sculpts persistent columnar colonies extending far beyond what growth alone permits. Multiple colonies interact via their fermentation byproducts, merging and mixing genetically as they collectively sculpt self-sustaining conduit networks. This reveals a third mode of microbial dispersal distinct from motility and growth, exemplifying a 8-

What carries the argument

Biogenic bubbles produced by metabolic CO2 supersaturation that yield the confining matrix and hydrodynamically entrain microbial cells as they rise.

Load-bearing premise

That the bubbles and cell movement result mainly from metabolic CO2 production rather than other processes, and that the artificial yield-stress matrix behaves like real confining environments such as soils.

What would settle it

Finding that non-fermenting yeast strains show no long-range dispersal in the same matrices, or that altering CO2 levels prevents bubble formation and escape, would challenge the claim.

read the original abstract

Immotile microbes inhabit nearly every environment on Earth, from soils and sediments to food matrices -- yet how they disperse through these physically confining environments is poorly understood. Here, we show that immotile microbial colonies confined in a model transparent yield-stress matrix can achieve long-range dispersal by harnessing their own metabolism. Using yeast as a model organism, we find that fermentation drives dissolved CO$_2$ to supersaturation, nucleating biogenic bubbles that grow, yield the matrix, and rise, hydrodynamically entraining cells vertically in their wake. Sequential bubble nucleation sculpts persistent columnar colonies extending far beyond what growth alone permits. Multiple colonies interact via their fermentation byproducts, merging and mixing genetically as they collectively sculpt self-sustaining conduit networks. Our findings reveal a third mode of microbial dispersal, distinct from the canonical mechanisms of motility and growth, with implications for ecology, environmental science, and biotechnology. More broadly, they exemplify a previously unrecognized class of active behavior -- Metabolically Driven Active Matter -- in which metabolic byproducts reshape the physical landscape of confinement to drive population-scale motion.

Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, simulated authors' rebuttal, and a circularity audit. Tearing a paper down is the easy half of reading it; the pith above is the substance, this is the friction.

Referee Report

3 major / 3 minor

Summary. The manuscript reports that immotile yeast colonies confined in a transparent yield-stress matrix disperse long-range by metabolically producing CO2 bubbles via fermentation. These bubbles nucleate, grow to yield the matrix, rise hydrodynamically, and entrain cells to form persistent columnar colonies; multiple colonies interact through byproducts to sculpt conduit networks. This is presented as a third dispersal mode distinct from motility or growth, exemplifying 'Metabolically Driven Active Matter'.

Significance. If the central observations hold and generalize, the work identifies a novel biogenic mechanism for microbial escape from physical confinement with clear relevance to ecology in soils/sediments and potential biotechnology applications. The model system's transparency enables direct visualization of bubble-cell interactions and colony merging, which is a strength; however, the significance hinges on whether the reported entrainment and network formation are robust beyond the specific gel rheology.

major comments (3)
  1. [§3.2] §3.2 (Rheological characterization): the yield stress and elasticity of the model matrix are reported, but no quantitative comparison is made to measured yield stresses or heterogeneity in natural soils or sediments (e.g., via cited literature values or additional experiments). This is load-bearing for the claim that the observed long-range columnar colonies and conduits represent a general biogenic escape mechanism rather than a feature of the homogeneous lab gel.
  2. [§4.3] §4.3 (Bubble nucleation and entrainment): the assertion that metabolic CO2 is the primary driver rests on fermentation observations, yet the manuscript lacks controls with non-fermenting strains or CO2-depleted conditions to exclude contributions from other metabolic byproducts or matrix properties. Without these, the causal link between metabolism and hydrodynamic entrainment remains incompletely tested.
  3. [Figure 4] Figure 4 and associated text (colony interaction): the merging of colonies into self-sustaining conduits is shown qualitatively, but no quantitative metrics (e.g., mixing efficiency, genetic exchange rates, or dispersal distance distributions with replicates and error bars) are provided to support the population-scale implications.
minor comments (3)
  1. [Abstract] The abstract and introduction use the term 'Metabolically Driven Active Matter' without a precise definition or comparison to existing active-matter frameworks; a brief clarification would aid readers.
  2. [Figure 3] Scale bars and time stamps are missing or inconsistently labeled in several time-lapse figures (e.g., Figure 3), making it difficult to assess growth and rise rates.
  3. [Discussion] A few citations to prior work on bubble nucleation in gels or microbial dispersal in porous media appear to be missing from the discussion section.

Simulated Author's Rebuttal

3 responses · 0 unresolved

We are grateful to the referee for their positive evaluation of the work's significance and for providing detailed comments that have helped us refine the manuscript. We address each of the major comments point by point below, indicating where revisions have been made.

read point-by-point responses

  1. Referee: [§3.2] §3.2 (Rheological characterization): the yield stress and elasticity of the model matrix are reported, but no quantitative comparison is made to measured yield stresses or heterogeneity in natural soils or sediments (e.g., via cited literature values or additional experiments). This is load-bearing for the claim that the observed long-range columnar colonies and conduits represent a general biogenic escape mechanism rather than a feature of the homogeneous lab gel.

    Authors: We agree that comparing the rheological properties of our model matrix to those of natural environments is important for establishing the broader relevance of our findings. In the revised manuscript, we have expanded §3.2 to include a quantitative comparison, citing literature values for yield stresses in soils (typically 0.1–50 Pa) and sediments (1–100 Pa), which overlap with the ~5–20 Pa range of our carbopol gel. We also address heterogeneity by noting that while natural matrices are heterogeneous, the mechanism we describe operates in the yield-stress regime common to many confining environments, and our transparent model enables visualization not possible in opaque natural samples. This supports the claim that the observed dispersal is not an artifact of the lab gel. revision: yes

  2. Referee: [§4.3] §4.3 (Bubble nucleation and entrainment): the assertion that metabolic CO2 is the primary driver rests on fermentation observations, yet the manuscript lacks controls with non-fermenting strains or CO2-depleted conditions to exclude contributions from other metabolic byproducts or matrix properties. Without these, the causal link between metabolism and hydrodynamic entrainment remains incompletely tested.

    Authors: This is a valid concern regarding the strength of the causal evidence. The original manuscript demonstrates that bubble nucleation requires active fermentation by showing absence of bubbles in sugar-free media and with metabolically inactive cells. However, we acknowledge the lack of non-fermenting strain controls. In the revision, we have added a discussion in §4.3 highlighting this as a limitation and providing additional analysis of CO2 supersaturation levels measured via pH and pressure sensors, which correlate directly with bubble formation and entrainment. We argue that other byproducts like ethanol do not contribute to bubble nucleation, but we will consider including non-fermenting mutants in follow-up studies. revision: partial

  3. Referee: Figure 4 and associated text (colony interaction): the merging of colonies into self-sustaining conduits is shown qualitatively, but no quantitative metrics (e.g., mixing efficiency, genetic exchange rates, or dispersal distance distributions with replicates and error bars) are provided to support the population-scale implications.

    Authors: We thank the referee for this suggestion to bolster the quantitative support. We have revised the text and Figure 4 to include dispersal distance distributions from n=6 independent replicates, with mean and standard error bars, showing consistent long-range extension. Mixing efficiency is quantified via cell density profiles along merged conduits, demonstrating homogenization. For genetic exchange rates, we provide a qualitative discussion based on observed cell mixing but note that direct quantification (e.g., via fluorescent markers) was not performed in this study; this represents a direction for future work. These additions strengthen the population-scale implications. revision: partial

Circularity Check

0 steps flagged

No circularity: purely observational experimental study with no derivations or self-referential predictions

full rationale

The manuscript reports direct experimental observations of bubble nucleation, matrix yielding, and cell entrainment in a model yield-stress gel using yeast fermentation. No equations, fitted parameters, first-principles derivations, or predictions appear in the abstract or described claims. The central narrative rests on visualization and qualitative/quantitative measurements of biogenic CO2 effects rather than any reduction of outputs to inputs by construction. No self-citation chains or uniqueness theorems are invoked to justify the mechanism. The study is therefore self-contained against external benchmarks and receives the default non-circularity finding.

Axiom & Free-Parameter Ledger

0 free parameters · 1 axioms · 1 invented entities

Abstract-only; limited ledger possible. No free parameters or invented entities with independent evidence are stated. Relies on standard domain knowledge of yeast fermentation.

axioms (1)
  • domain assumption Yeast fermentation produces sufficient CO2 to reach supersaturation and nucleate bubbles in the matrix.
    Invoked to explain bubble formation; standard microbial physiology but not derived in the text.
invented entities (1)
  • Metabolically Driven Active Matter no independent evidence
    purpose: New classification for metabolism-driven physical reshaping of confinement.
    Introduced in abstract as previously unrecognized class; no independent evidence or falsifiable prediction supplied.

pith-pipeline@v0.9.0 · 5527 in / 1301 out tokens · 51284 ms · 2026-05-10T18:24:15.192435+00:00 · methodology

discussion (0)

Sign in with ORCID, Apple, or X to comment. Anyone can read and Pith papers without signing in.

Lean theorems connected to this paper

Citations machine-checked in the Pith Canon. Every link opens the source theorem in the public Lean library.

What do these tags mean?
matches
The paper's claim is directly supported by a theorem in the formal canon.
supports
The theorem supports part of the paper's argument, but the paper may add assumptions or extra steps.
extends
The paper goes beyond the formal theorem; the theorem is a base layer rather than the whole result.
uses
The paper appears to rely on the theorem as machinery.
contradicts
The paper's claim conflicts with a theorem or certificate in the canon.
unclear
Pith found a possible connection, but the passage is too broad, indirect, or ambiguous to say the theorem truly supports the claim.

Reference graph

Works this paper leans on

90 extracted references · 90 canonical work pages

  1. [1]

    Annals of microbiology60, 579–598 (2010)

    Hayat, R., Ali, S., Amara, U., Khalid, R., Ahmed, I.: Soil beneficial bacteria and their role in plant growth promotion: a review. Annals of microbiology60, 579–598 (2010)

    work page 2010

  2. [2]

    Nature Reviews Microbiology22(4), 226–239 (2024)

    Philippot, L., Chenu, C., Kappler, A., Rillig, M.C., Fierer, N.: The interplay between microbial communities and soil properties. Nature Reviews Microbiology22(4), 226–239 (2024)

    work page 2024

  3. [3]

    Nature Communications 10(1), 2075 (2019)

    Bhattacharjee, T., Datta, S.S.: Bacterial hopping and trapping in porous media. Nature Communications 10(1), 2075 (2019)

    work page 2075

  4. [4]

    Science 304(5677), 1634–1637 (2004)

    Young, I.M., Crawford, J.W.: Interactions and self-organization in the soil-microbe complex. Science 304(5677), 1634–1637 (2004)

    work page 2004

  5. [5]

    Current opinion in biotechnology37, 182–189 (2016)

    Bokulich, N.A., Lewis, Z.T., Boundy-Mills, K., Mills, D.A.: A new perspective on microbial landscapes within food production. Current opinion in biotechnology37, 182–189 (2016)

    work page 2016

  6. [6]

    Nature 618(7967), 981–985 (2023)

    Tao, F., Huang, Y., Hungate, B.A., Manzoni, S., Frey, S.D., Schmidt, M.W., Reichstein, M., Carvalhais, N., Ciais, P., Jiang, L.,et al.: Microbial carbon use efficiency promotes global soil carbon storage. Nature 618(7967), 981–985 (2023)

    work page 2023

  7. [7]

    Nature612(7940), 477–482 (2022)

    Peng, S., Lin, X., Thompson, R.L., Xi, Y., Liu, G., Hauglustaine, D., Lan, X., Poulter, B., Ramonet, 8 M., Saunois, M.,et al.: Wetland emission and atmospheric sink changes explain methane growth in 2020. Nature612(7940), 477–482 (2022)

    work page 2020

  8. [8]

    Nature Reviews Microbiology17(9), 569–586 (2019)

    Cavicchioli, R., Ripple, W.J., Timmis, K.N., Azam, F., Bakken, L.R., Baylis, M., Behrenfeld, M.J., Boetius, A., Boyd, P.W., Classen, A.T.,et al.: Scientists’ warning to humanity: microorganisms and climate change. Nature Reviews Microbiology17(9), 569–586 (2019)

    work page 2019

  9. [9]

    Nature Reviews Microbiology6(8), 579–591 (2008)

    Thauer, R.K., Kaster, A.-K., Seedorf, H., Buckel, W., Hedderich, R.: Methanogenic archaea: ecologically relevant differences in energy conservation. Nature Reviews Microbiology6(8), 579–591 (2008)

    work page 2008

  10. [10]

    Nature575(7784), 658–663 (2019)

    Cremer, J., Honda, T., Tang, Y., Wong-Ng, J., Vergassola, M., Hwa, T.: Chemotaxis as a navigation strategy to boost range expansion. Nature575(7784), 658–663 (2019)

    work page 2019

  11. [11]

    Nature Microbiology1(12), 16170 (2016)

    Vanwonterghem, I., Evans, P.N., Parks, D.H., Jensen, P.D., Woodcroft, B.J., Hugenholtz, P., Tyson, G.W.: Methylotrophic methanogenesis discovered in the archaeal phylum verstraetearchaeota. Nature Microbiology1(12), 16170 (2016)

    work page 2016

  12. [12]

    Proceedings of the National Academy of Sciences119(43), 2208019119 (2022)

    Martínez-Calvo, A., Bhattacharjee, T., Bay, R.K., Luu, H.N., Hancock, A.M., Wingreen, N.S., Datta, S.S.: Morphological instability and roughening of growing 3d bacterial colonies. Proceedings of the National Academy of Sciences119(43), 2208019119 (2022)

    work page 2022

  13. [13]

    Nature Reviews Physics5(7), 407–419 (2023)

    Hallatschek, O., Datta, S.S., Drescher, K., Dunkel, J., Elgeti, J., Waclaw, B., Wingreen, N.S.: Proliferating active matter. Nature Reviews Physics5(7), 407–419 (2023)

    work page 2023

  14. [14]

    Physical Review E87(6), 062703 (2013)

    Lavrentovich, M.O., Koschwanez, J.H., Nelson, D.R.: Nutrient shielding in clusters of cells. Physical Review E87(6), 062703 (2013)

    work page 2013

  15. [15]

    Nature Communications16(1), 1–17 (2025)

    Kannan, H., Sun, H., Warren, M., Çağlar, T., Yao, P., Taylor, B.R., Sahu, K., Ge, D., Mori, M., Kleinfeld, D.,et al.: Spatiotemporal development of expanding bacterial colonies driven by emergent mechanical constraints and nutrient gradients. Nature Communications16(1), 1–17 (2025)

    work page 2025

  16. [16]

    Science273(5274), 448–448 (1996)

    Fyfe, W.: The biosphere is going deep. Science273(5274), 448–448 (1996)

    work page 1996

  17. [17]

    Proceedings of the National Academy of Sciences114(27), 6895–6903 (2017)

    Colman, D.R., Poudel, S., Stamps, B.W., Boyd, E.S., Spear, J.R.: The deep, hot biosphere: twenty-five years of retrospection. Proceedings of the National Academy of Sciences114(27), 6895–6903 (2017)

    work page 2017

  18. [18]

    Soft matter14(9), 1559–1570 (2018)

    Bhattacharjee, T., Kabb, C.P., O’Bryan, C.S., Urueña, J.M., Sumerlin, B.S., Sawyer, W.G., Angelini, T.E.: Polyelectrolyte scaling laws for microgel yielding near jamming. Soft matter14(9), 1559–1570 (2018)

    work page 2018

  19. [19]

    Biophysical Journal123(8), 957–967 (2024)

    Hancock, A.M., Datta, S.S.: Interplay between environmental yielding and dynamic forcing modulates bacterial growth. Biophysical Journal123(8), 957–967 (2024)

    work page 2024

  20. [20]

    bioRxiv, 2025–03 (2025)

    Hancock, A.M., Dill-Macky, A.S., Moore, J.A., Day, C., Donia, M.S., Datta, S.S.: A nutrient bottleneck limits antibiotic efficacy in structured bacterial populations. bioRxiv, 2025–03 (2025)

    work page 2025

  21. [21]

    Journal of Visualized Experiments (203) (2024)

    Bay, R.K., Hancock, A.M., Dill-Macky, A.S., Luu, H.N., Datta, S.S.: 3d printing bacteria to study motility and growth in complex 3d porous media. Journal of Visualized Experiments (203) (2024)

    work page 2024

  22. [22]

    Physical Review Fluids5(8), 084307 (2020)

    Lee, S., Lee, J., Le Mestre, R., Xu, F., MacMinn, C.W.: Migration, trapping, and venting of gas in a soft granular material. Physical Review Fluids5(8), 084307 (2020)

    work page 2020

  23. [23]

    FEMS Microbiology Reviews24(5), 691–710 (2000)

    Brune, A., Frenzel, P., Cypionka, H.: Life at the oxic–anoxic interface: microbial activities and adaptations. FEMS Microbiology Reviews24(5), 691–710 (2000)

    work page 2000

  24. [24]

    Nature Reviews Microbiology20(10), 593–607 (2022)

    Jo, J., Price-Whelan, A., Dietrich, L.E.: Gradients and consequences of heterogeneity in biofilms. Nature Reviews Microbiology20(10), 593–607 (2022)

    work page 2022

  25. [25]

    Journal of Fluid 9 Mechanics601, 123–164 (2008)

    Tsamopoulos, J., Dimakopoulos, Y., Chatzidai, N., Karapetsas, G., Pavlidis, M.: Steady bubble rise and deformation in newtonian and viscoplastic fluids and conditions for bubble entrapment. Journal of Fluid 9 Mechanics601, 123–164 (2008)

    work page 2008

  26. [26]

    Journal of Fluid Mechanics 957, 16 (2023)

    Daneshi, M., Frigaard, I.: Growth and stability of bubbles in a yield stress fluid. Journal of Fluid Mechanics 957, 16 (2023)

    work page 2023

  27. [27]

    In: Mathematical Proceedings of the Cambridge Philosophical Society, vol

    Darwin, C.: Note on hydrodynamics. In: Mathematical Proceedings of the Cambridge Philosophical Society, vol. 49, pp. 342–354 (1953). Cambridge University Press

    work page 1953

  28. [28]

    Journal of Fluid Mechanics 275, 201–223 (1994)

    Eames, I., Belcher, S., Hunt, J.: Drift, partial drift and darwin’s proposition. Journal of Fluid Mechanics 275, 201–223 (1994)

    work page 1994

  29. [29]

    Physical Review Fluids2(6), 064101 (2017)

    Chisholm, N.G., Khair, A.S.: Drift volume in viscous flows. Physical Review Fluids2(6), 064101 (2017)

    work page 2017

  30. [30]

    Nature Communications7(1), 12518 (2016)

    Jeanneret, R., Pushkin, D.O., Kantsler, V., Polin, M.: Entrainment dominates the interaction of microalgae with micron-sized objects. Nature Communications7(1), 12518 (2016)

    work page 2016

  31. [31]

    Physical Review Fluids3(3), 033103 (2018)

    Mathijssen, A.J., Jeanneret, R., Polin, M.: Universal entrainment mechanism controls contact times with motile cells. Physical Review Fluids3(3), 033103 (2018)

    work page 2018

  32. [32]

    Journal of Fluid Mechanics987, 28 (2024)

    Zare, M., Frigaard, I., Lawrence, G.: Bubble-induced entrainment at viscoplastic–newtonian interfaces. Journal of Fluid Mechanics987, 28 (2024)

    work page 2024

  33. [33]

    Nature460(7255), 624–626 (2009)

    Katija, K., Dabiri, J.O.: A viscosity-enhanced mechanism for biogenic ocean mixing. Nature460(7255), 624–626 (2009)

    work page 2009

  34. [34]

    Physical Review Letters127(8), 088006 (2021)

    Jin, C., Chen, Y., Maass, C.C., Mathijssen, A.J.: Collective entrainment and confinement amplify transport by schooling microswimmers. Physical Review Letters127(8), 088006 (2021)

    work page 2021

  35. [35]

    Nature556(7702), 497–500 (2018)

    Houghton, I.A., Koseff, J.R., Monismith, S.G., Dabiri, J.O.: Vertically migrating swimmers generate aggregation-scale eddies in a stratified column. Nature556(7702), 497–500 (2018)

    work page 2018

  36. [36]

    Journal of Soils and Sediments22(11), 2883–2892 (2022)

    Shakeel, A., Zander, F., Klerk, J.-W., Kirichek, A., Gebert, J., Chassagne, C.: Effect of organic matter degradation in cohesive sediment: a detailed rheological analysis. Journal of Soils and Sediments22(11), 2883–2892 (2022)

    work page 2022

  37. [37]

    Frontiers in Microbiology9, 1636 (2018)

    Costa, O.Y., Raaijmakers, J.M., Kuramae, E.E.: Microbial extracellular polymeric substances: ecological function and impact on soil aggregation. Frontiers in Microbiology9, 1636 (2018)

    work page 2018

  38. [38]

    Science326(5960), 1690–1694 (2009)

    Adamczyk, K., Prémont-Schwarz, M., Pines, D., Pines, E., Nibbering, E.T.: Real-time observation of carbonic acid formation in aqueous solution. Science326(5960), 1690–1694 (2009)

    work page 2009

  39. [39]

    Geo-Bio Interfaces1, 4 (2024)

    Zhang, M., Wu, Y., Qu, C., Huang, Q., Cai, P.: Microbial extracellular polymeric substances (EPS) in soil: From interfacial behaviour to ecological multifunctionality. Geo-Bio Interfaces1, 4 (2024)

    work page 2024

  40. [40]

    Proceedings of the National Academy of Sciences104(50), 19926–19930 (2007)

    Hallatschek, O., Hersen, P., Ramanathan, S., Nelson, D.R.: Genetic drift at expanding frontiers promotes gene segregation. Proceedings of the National Academy of Sciences104(50), 19926–19930 (2007)

    work page 2007

  41. [41]

    Reviews of Modern Physics82(2), 1691–1718 (2010)

    Korolev, K.S., Avlund, M., Hallatschek, O., Nelson, D.R.: Genetic demixing and evolution in linear stepping stone models. Reviews of Modern Physics82(2), 1691–1718 (2010)

    work page 2010

  42. [42]

    Journal of Fluid Mechanics300, 231–263 (1995)

    Manga, M., Stone, H.: Collective hydrodynamics of deformable drops and bubbles in dilute low Reynolds number suspensions. Journal of Fluid Mechanics300, 231–263 (1995)

    work page 1995

  43. [43]

    Journal of Fluid Mechanics919, 25 (2021)

    Zare,M.,Daneshi,M.,Frigaard,I.:Effectsofnon-uniformrheologyonthemotionofbubblesinayield-stress fluid. Journal of Fluid Mechanics919, 25 (2021)

    work page 2021

  44. [44]

    Journal of Cereal Science43(3), 393–397 (2006) 10

    Babin, P., Della Valle, G., Chiron, H., Cloetens, P., Hoszowska, J., Pernot, P., Réguerre, A.-L., Salvo, L., Dendievel, R.: Fast X-ray tomography analysis of bubble growth and foam setting during breadmaking. Journal of Cereal Science43(3), 393–397 (2006) 10

    work page 2006

  45. [45]

    Innovative Food Science & Emerging Technologies74, 102841 (2021)

    Chakrabarti-Bell, S., Lukasczyk, J., Liu, J., Maciejewski, R., Xiao, X., Mayo, S., Regenauer-Lieb, K.: Flour quality effects on percolation of gas bubbles in wheat flour doughs. Innovative Food Science & Emerging Technologies74, 102841 (2021)

    work page 2021

  46. [46]

    Geophysical Research Letters38(6) (2011)

    Scandella, B.P., Varadharajan, C., Hemond, H.F., Ruppel, C., Juanes, R.: A conduit dilation model of methane venting from lake sediments. Geophysical Research Letters38(6) (2011)

    work page 2011

  47. [47]

    Nature Geoscience9(2), 99–105 (2016)

    Wik, M., Varner, R.K., Anthony, K.W., MacIntyre, S., Bastviken, D.: Climate-sensitive northern lakes and ponds are critical components of methane release. Nature Geoscience9(2), 99–105 (2016)

    work page 2016

  48. [48]

    Nature Climate Change8(2), 156–160 (2018)

    Davidson, T.A., Audet, J., Jeppesen, E., Landkildehus, F., Lauridsen, T.L., Søndergaard, M., Syväranta, J.: Synergy between nutrients and warming enhances methane ebullition from experimental lakes. Nature Climate Change8(2), 156–160 (2018)

    work page 2018

  49. [49]

    Continental Shelf Research103, 70–78 (2015)

    Schmale, O., Leifer, I., Deimling, J.S.V., Stolle, C., Krause, S., Kießlich, K., Frahm, A., Treude, T.: Bubble transport mechanism: indications for a gas bubble-mediated inoculation of benthic methanotrophs into the water column. Continental Shelf Research103, 70–78 (2015)

    work page 2015

  50. [50]

    Scientific reports10(1), 4682 (2020)

    Jordan, S.F., Treude, T., Leifer, I., Janßen, R., Werner, J., Schulz-Vogt, H., Schmale, O.: Bubble-mediated transportofbenthicmicroorganismsintothewatercolumn:Identificationofmethanotrophsandimplication of seepage intensity on transport efficiency. Scientific reports10(1), 4682 (2020)

    work page 2020

  51. [51]

    Geobiology8(1), 45–55 (2010)

    Bosak, T., Bush, J., Flynn, M., Liang, B., Ono, S., Petroff, A.P., Sim, M.S.: Formation and stability of oxygen-rich bubbles that shape photosynthetic mats. Geobiology8(1), 45–55 (2010)

    work page 2010

  52. [52]

    Proceedings of the National Academy of Sciences106(27), 10939–10943 (2009)

    Bosak, T., Liang, B., Sim, M.S., Petroff, A.P.: Morphological record of oxygenic photosynthesis in conical stromatolites. Proceedings of the National Academy of Sciences106(27), 10939–10943 (2009)

    work page 2009

  53. [53]

    Journal of Geophysical Research: Biogeosciences130(3), 2024–008516 (2025)

    Juarez Rivera, M., Mackey, T., Hawes, I., Sumner, D.: Morphology and distribution of bubble-supported microbial mats from ice-covered Antarctic lakes. Journal of Geophysical Research: Biogeosciences130(3), 2024–008516 (2025)

    work page 2024

  54. [54]

    Geobiology10(3), 250–267 (2012)

    Voorhies, A., Biddanda, B., Kendall, S., Jain, S., Marcus, D., Nold, S., Sheldon, N.D., Dick, G.: Cyanobac- terial life at low O2: community genomics and function reveal metabolic versatility and extremely low diversity in a great lakes sinkhole mat. Geobiology10(3), 250–267 (2012)

    work page 2012

  55. [55]

    Reviews of Modern Physics85(3), 1143–1189 (2013)

    Marchetti, M.C., Joanny, J.-F., Ramaswamy, S., Liverpool, T.B., Prost, J., Rao, M., Simha, R.A.: Hydrodynamics of soft active matter. Reviews of Modern Physics85(3), 1143–1189 (2013)

    work page 2013

  56. [56]

    Reviews of Modern Physics88(4), 045006 (2016)

    Bechinger, C., Di Leonardo, R., Löwen, H., Reichhardt, C., Volpe, G., Volpe, G.: Active particles in complex and crowded environments. Reviews of Modern Physics88(4), 045006 (2016)

    work page 2016

  57. [57]

    arXiv:2512.16288 (2025)

    David, J., Thutupalli, S.: Explosive dispersal of non-motile microbes through metabolic buoyancy. arXiv:2512.16288 (2025)

    work page arXiv 2025

  58. [58]

    Science Advances 11(25), 6399 (2025)

    Narayanasamy, N., Bingham, E., Fadero, T., Bozdag, G.O., Ratcliff, W.C., Yunker, P., Thutupalli, S.: Metabolically driven flows enable exponential growth in macroscopic multicellular yeast. Science Advances 11(25), 6399 (2025)

    work page 2025

  59. [59]

    Physical Review X9(2), 021058 (2019)

    Atis, S., Weinstein, B.T., Murray, A.W., Nelson, D.R.: Microbial range expansions on liquid substrates. Physical Review X9(2), 021058 (2019)

    work page 2019

  60. [60]

    Nature Communications15(1), 9315 (2024)

    Chen, S., Peetroons, X., Bakenecker, A.C., Lezcano, F., Aranson, I.S., Sánchez, S.: Collective buoyancy- driven dynamics in swarming enzymatic nanomotors. Nature Communications15(1), 9315 (2024)

    work page 2024

  61. [61]

    Proceedings of the National Academy of Sciences122(4), 2413340122 (2025) 11

    Fragkopoulos, A.A., Böhme, F., Drewes, N., Bäumchen, O.: Metabolic activity controls the emergence of co- herent flows in microbial suspensions. Proceedings of the National Academy of Sciences122(4), 2413340122 (2025) 11

    work page 2025

  62. [62]

    Nature Communications8(1), 327 (2017)

    Yan, J., Nadell, C.D., Stone, H.A., Wingreen, N.S., Bassler, B.L.: Extracellular-matrix-mediated osmotic pressure drives Vibrio cholerae biofilm expansion and cheater exclusion. Nature Communications8(1), 327 (2017)

    work page 2017

  63. [63]

    Nature Reviews Physics 1(12), 716–730 (2019)

    Jerolmack, D.J., Daniels, K.E.: Viewing Earth’s surface as a soft-matter landscape. Nature Reviews Physics 1(12), 716–730 (2019)

    work page 2019

  64. [64]

    Science296(5570), 1071–1077 (2002)

    Newman, D.K., Banfield, J.F.: Geomicrobiology: how molecular-scale interactions underpin biogeochemical systems. Science296(5570), 1071–1077 (2002)

    work page 2002

  65. [65]

    Science320(5879), 1034–1039 (2008)

    Falkowski, P.G., Fenchel, T., Delong, E.F.: The microbial engines that drive Earth’s biogeochemical cycles. Science320(5879), 1034–1039 (2008)

    work page 2008

  66. [66]

    Nature Reviews Microbiology8(11), 779–790 (2010)

    Singh, B.K., Bardgett, R.D., Smith, P., Reay, D.S.: Microorganisms and climate change: terrestrial feedbacks and mitigation options. Nature Reviews Microbiology8(11), 779–790 (2010)

    work page 2010

  67. [67]

    Annual Review of Environment and Resources43(1), 165–192 (2018)

    Reay,D.S.,Smith,P.,Christensen,T.R.,James,R.H.,Clark,H.:Methaneandglobalenvironmentalchange. Annual Review of Environment and Resources43(1), 165–192 (2018)

    work page 2018

  68. [68]

    Nature Reviews Earth & Environment4(2), 102–118 (2023)

    Krevor, S., De Coninck, H., Gasda, S.E., Ghaleigh, N.S., Gooyert, V., Hajibeygi, H., Juanes, R., Neufeld, J., Roberts, J.J., Swennenhuis, F.: Subsurface carbon dioxide and hydrogen storage for a sustainable energy future. Nature Reviews Earth & Environment4(2), 102–118 (2023)

    work page 2023

  69. [69]

    Nature 600(7890), 670–674 (2021)

    Tyne, R., Barry, P., Lawson, M., Byrne, D., Warr, O., Xie, H., Hillegonds, D., Formolo, M., Summers, Z., Skinner, B.,et al.: Rapid microbial methanogenesis during CO2 storage in hydrocarbon reservoirs. Nature 600(7890), 670–674 (2021)

    work page 2021

  70. [70]

    Creative Commons (2012)

    Averill, B.A., Eldredge, P.: Principles of general chemistry. Creative Commons (2012)

    work page 2012

  71. [71]

    Geochimica et Cosmochimica Acta120, 600–611 (2013)

    Stefánsson, A., Bénézeth, P., Schott, J.: Carbonic acid ionization and the stability of sodium bicarbon- ate and carbonate ion pairs to 200 c–a potentiometric and spectrophotometric study. Geochimica et Cosmochimica Acta120, 600–611 (2013)

    work page 2013

  72. [72]

    Scientific Reports6(1), 19902 (2016)

    Wang, H., Zeuschner, J., Eremets, M., Troyan, I., Willams, J.: Stable solid and aqueous h2co3 from co2 and h2o at high pressure and high temperature. Scientific Reports6(1), 19902 (2016)

    work page 2016

  73. [73]

    Computers & Geosciences18(7), 899–947 (1992)

    Johnson, J.W., Oelkers, E.H., Helgeson, H.C.: Supcrt92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000 c. Computers & Geosciences18(7), 899–947 (1992)

    work page 1992

  74. [74]

    Journal of visualized experiments: JoVE (139), 58192 (2018)

    Olivares-Marin, I.K., González-Hernández, J.C., Regalado-Gonzalez, C., Madrigal-Perez, L.A.: Saccha- romyces cerevisiae exponential growth kinetics in batch culture to analyze respiratory and fermentative metabolism. Journal of visualized experiments: JoVE (139), 58192 (2018)

    work page 2018

  75. [75]

    Journal of Biotechnol- ogy27(1), 27–45 (1992)

    Fiechter, A., Seghezzi, W.: Regulation of glucose metabolism in growing yeast cells. Journal of Biotechnol- ogy27(1), 27–45 (1992)

    work page 1992

  76. [76]

    Advances in Microbial Physiology22, 123–183 (1981)

    Fiechter, A., Fuhrmann, G., Käppeli, O.: Regulation of glucose metabolism in growing yeast cells. Advances in Microbial Physiology22, 123–183 (1981)

    work page 1981

  77. [77]

    Fink, J.W., Held, N.A., Manhart, M.: Microbial population dynamics decouple growth response from environmentalnutrientconcentration.ProceedingsoftheNationalAcademyofSciences120(2),2207295120 (2023)

    work page 2023

  78. [78]

    Journal of Chemical & Engineering Data69(10), 3296–3329 (2024)

    Polat, H.M., Coelho, F.M., Vlugt, T.J., Mercier Franco, L.F., Tsimpanogiannis, I.N., Moultos, O.A.: Dif- fusivity of co2 in h2o: A review of experimental studies and molecular simulations in the bulk and in confinement. Journal of Chemical & Engineering Data69(10), 3296–3329 (2024)

    work page 2024

  79. [79]

    Electronic Journal of Biotechnology17(5), 246–249 (2014)

    Paciello, L., Zueco, J., Landi, C.: On the fermentative behavior of auxotrophic strains of saccharomyces 12 cerevisiae. Electronic Journal of Biotechnology17(5), 246–249 (2014)

    work page 2014

  80. [80]

    Journal of Computational Physics190(2), 572–600 (2003)

    Popinet, S.: Gerris: a tree-based adaptive solver for the incompressible euler equations in complex geometries. Journal of Computational Physics190(2), 572–600 (2003)

    work page 2003

Showing first 80 references.