in

The ecological roles of bacterial chemotaxis

  • Wadhwa, N. & Berg, H. C. Bacterial motility: machinery and mechanisms. Nat. Rev. Microbiol. 20, 161–173 (2022). This recent review provides an excellent overview of the diversity in bacterial propulsion mechanisms.

    CAS 
    PubMed 

    Google Scholar 

  • Burrows, L. L. Pseudomonas aeruginosa twitching motility: type IV pili in action. Annu. Rev. Microbiol. 66, 493–520 (2012).

    CAS 
    PubMed 

    Google Scholar 

  • Dufrêne, Y. F. & Persat, A. Mechanomicrobiology: how bacteria sense and respond to forces. Nat. Rev. Microbiol. 18, 227–240 (2020).

    PubMed 

    Google Scholar 

  • Jarrell, K. F. & McBride, M. J. The surprisingly diverse ways that prokaryotes move. Nat. Rev. Microbiol. 6, 466–476 (2008).

    CAS 
    PubMed 

    Google Scholar 

  • Berg, H. C. E. coli in Motion (Springer, 2004).

  • Bi, S. & Sourjik, V. Stimulus sensing and signal processing in bacterial chemotaxis. Curr. Opin. Microbiol. 45, 22–29 (2018).

    CAS 
    PubMed 

    Google Scholar 

  • Parkinson, J. S., Hazelbauer, G. L. & Falke, J. J. Signaling and sensory adaptation in Escherichia coli chemoreceptors: 2015 update. Trends Microbiol. 23, 257–266 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Porter, S. L., Wadhams, G. H. & Armitage, J. P. Signal processing in complex chemotaxis pathways. Nat. Rev. Microbiol. 9, 153–165 (2011).

    CAS 
    PubMed 

    Google Scholar 

  • Colin, R. & Sourjik, V. Emergent properties of bacterial chemotaxis pathway. Curr. Opin. Microbiol. 39, 24–33 (2017).

    CAS 
    PubMed 

    Google Scholar 

  • Brumley, D. R. et al. Cutting through the noise: bacterial chemotaxis in marine microenvironments. Front. Mar. Sci. 7, 527 (2020).

    Google Scholar 

  • Hein, A. M., Carrara, F., Brumley, D. R., Stocker, R. & Levin, S. A. Natural search algorithms as a bridge between organisms, evolution, and ecology. Proc. Natl Acad. Sci. USA 113, 9413–9420 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wong-Ng, J., Celani, A. & Vergassola, M. Exploring the function of bacterial chemotaxis. Curr. Opin. Microbiol. 45, 16–21 (2018).

    CAS 
    PubMed 

    Google Scholar 

  • Colin, R., Ni, B., Laganenka, L. & Sourjik, V. Multiple functions of flagellar motility and chemotaxis in bacterial physiology. FEMS Microbiol. Rev. 45, fuab038 (2021).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Schweinitzer, T. & Josenhans, C. Bacterial energy taxis: a global strategy? Arch. Microbiol. 192, 507–520 (2010).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Somavanshi, R., Ghosh, B. & Sourjik, V. Sugar influx sensing by the phosphotransferase system of Escherichia coli. PLoS Biol. 14, e2000074 (2016).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Cremer, J. et al. Chemotaxis as a navigation strategy to boost range expansion. Nature 575, 658–663 (2019). This work uses a quantitative approach to describe the classic assay of bacterial growth and migration in soft agar, and elucidates the distinct roles of attractant and nutrient in colony expansion.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Raina, J.-B., Fernandez, V., Lambert, B., Stocker, R. & Seymour, J. R. The role of microbial motility and chemotaxis in symbiosis. Nat. Rev. Microbiol. 17, 284–294 (2019). This study presents a comprehensive overview of the role of bacterial motility and chemotaxis in establishing and maintaining symbiotic relationships.

    CAS 
    PubMed 

    Google Scholar 

  • Matilla, M. A. & Krell, T. The effect of bacterial chemotaxis on host infection and pathogenicity. FEMS Microbiol. Rev. 42, fux052 (2018). This work presents an extensive review of the role of bacterial motility and chemotaxis in host pathogenicity from plants to animals.

    Google Scholar 

  • Perkins, A., Tudorica, D. A., Amieva, M. R., Remington, S. J. & Guillemin, K. Helicobacter pylori senses bleach (HOCl) as a chemoattractant using a cytosolic chemoreceptor. PLoS Biol. 17, e3000395 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Tohidifar, P. et al. The unconventional cytoplasmic sensing mechanism for ethanol chemotaxis in Bacillus subtilis. mBio 11, e02177-20 (2020).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Kundu, P., Blacher, E., Elinav, E. & Pettersson, S. Our gut microbiome: the evolving inner self. Cell 171, 1481–1493 (2017).

    CAS 
    PubMed 

    Google Scholar 

  • Azam, F. & Malfatti, F. Microbial structuring of marine ecosystems. Nat. Rev. Microbiol. 5, 782–791 (2007).

    CAS 
    PubMed 

    Google Scholar 

  • Buchan, A., LeCleir, G. R., Gulvik, C. A. & González, J. M. Master recyclers: features and functions of bacteria associated with phytoplankton blooms. Nat. Rev. Microbiol. 12, 686–698 (2014).

    CAS 
    PubMed 

    Google Scholar 

  • Savageau, M. A. Escherichia coli habitats, cell types and molecular mechanisms of gene control. Am. Nat. 122, 732–744 (1983).

    CAS 

    Google Scholar 

  • Vorholt, J. A. Microbial life in the phyllosphere. Nat. Rev. Microbiol. 10, 828–840 (2012).

    CAS 
    PubMed 

    Google Scholar 

  • Scharf, B. E., Hynes, M. F. & Alexandre, G. M. Chemotaxis signaling systems in model beneficial plant–bacteria associations. Plant. Mol. Biol. 90, 549–559 (2016).

    CAS 
    PubMed 

    Google Scholar 

  • Stocker, R. & Seymour, J. R. Ecology and physics of bacterial chemotaxis in the ocean. Microbiol. Mol. Biol. Rev. 76, 792–812 (2012).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Datta, M. S., Sliwerska, E., Gore, J., Polz, M. F. & Cordero, O. X. Microbial interactions lead to rapid micro-scale successions on model marine particles. Nat. Commun. 7, 11965 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Barbara, G. M. & Mitchell, J. G. Bacterial tracking of motile algae. FEMS Microbiol. Ecol. 44, 79–87 (2003).

    CAS 
    PubMed 

    Google Scholar 

  • Garren, M. et al. A bacterial pathogen uses dimethylsulfoniopropionate as a cue to target heat-stressed corals. ISME J. 8, 999–1007 (2014).

    CAS 
    PubMed 

    Google Scholar 

  • Szurmant, H. & Ordal, G. W. Diversity in chemotaxis mechanisms among the bacteria and archaea. Microbiol. Mol. Biol. Rev. 68, 301–319 (2004).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wuichet, K. & Zhulin, I. B. Origins and diversification of a complex signal transduction system in prokaryotes. Sci. Signal. 3, ra50 (2010).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Zehr, J. P., Weitz, J. S. & Joint, I. How microbes survive in the open ocean. Science 357, 646–647 (2017).

    CAS 
    PubMed 

    Google Scholar 

  • McDougald, D., Rice, S. A., Barraud, N., Steinberg, P. D. & Kjelleberg, S. Should we stay or should we go: mechanisms and ecological consequences for biofilm dispersal. Nat. Rev. Microbiol. 10, 39–50 (2012).

    CAS 

    Google Scholar 

  • Yawata, Y., Carrara, F., Menolascina, F. & Stocker, R. Constrained optimal foraging by marine bacterioplankton on particulate organic matter. Proc. Natl Acad. Sci. USA 117, 25571–25579 (2020). This study reveals that a marine bacterium foraging on particulate nutrient hotspots optimizes nutrient uptake using rapid switches between chemotactic and non-motile lifestyles.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Paul, K., Nieto, V., Carlquist, W. C., Blair, D. F. & Harshey, R. M. The c-di-GMP binding protein YcgR controls flagellar motor direction and speed to affect chemotaxis by a “backstop brake” mechanism. Mol. Cell 38, 128–139 (2010).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Fenchel, T. Microbial behavior in a heterogeneous world. Science 296, 1068–1071 (2002).

    CAS 
    PubMed 

    Google Scholar 

  • Stocker, R. Marine microbes see a sea of gradients. Science 338, 628–633 (2012).

    CAS 

    Google Scholar 

  • McDonald, D. E., Pethick, D. W., Mullan, B. P. & Hampson, D. J. Increasing viscosity of the intestinal contents alters small intestinal structure and intestinal growth, and stimulates proliferation of enterotoxigenic Escherichia coli in newly-weaned pigs. Br. J. Nutr. 86, 487–498 (2001).

    CAS 
    PubMed 

    Google Scholar 

  • Berg, H. C. & Turner Movement of microorganisms in viscous environments. Nature 278, 349–351 (1979).

    CAS 
    PubMed 

    Google Scholar 

  • Borer, B., Tecon, R. & Or, D. Spatial organization of bacterial populations in response to oxygen and carbon counter-gradients in pore networks. Nat. Commun. 9, 769 (2018).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Whitman, W. B., Coleman, D. C. & Wiebe, W. J. Prokaryotes: the unseen majority. Proc. Natl Acad. Sci. USA 95, 6578–6583 (1998).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Raynaud, X. & Nunan, N. Spatial ecology of bacteria at the microscale in soil. PLoS ONE 9, e87217 (2014).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Lindow, S. E. & Brandl, M. T. Microbiology of the phyllosphere. Appl. Env. Microbiol. 69, 9 (2003).

    Google Scholar 

  • Fernandez, V. I., Yawata, Y. & Stocker, R. A foraging mandala for aquatic microorganisms. ISME J. 13, 563–575 (2019).

    PubMed 

    Google Scholar 

  • Purcell, E. M. Life at low Reynolds number. Am. J. Phys. 45, 10 (1977).

    Google Scholar 

  • Dusenbery, D. B. Living at Micro Scale: The Unexpected Physics of Being Small (Harvard Univ. Press, 2011).

  • Phillips, R. & Milo, R. Cell Biology by the Numbers (Garland Science, 2015).

  • Darnton, N. C., Turner, L., Rojevsky, S. & Berg, H. C. On torque and tumbling in swimming Escherichia coli. J. Bacteriol. 189, 1756–1764 (2007).

    CAS 
    PubMed 

    Google Scholar 

  • Ryu, W. S., Berry, R. M. & Berg, H. C. Torque-generating units of the flagellar motor of Escherichia coli have a high duty ratio. Nature 403, 444–446 (2000).

    CAS 
    PubMed 

    Google Scholar 

  • Chattopadhyay, S., Moldovan, R., Yeung, C. & Wu, X. L. Swimming efficiency of bacterium Escherichia coli. Proc. Natl Acad. Sci. USA 103, 13712–13717 (2006).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Sowa, Y., Hotta, H., Homma, M. & Ishijima, A. Torque–speed relationship of the Na+-driven flagellar motor of Vibrio alginolyticus. J. Mol. Biol. 327, 1043–1051 (2003).

    CAS 
    PubMed 

    Google Scholar 

  • Taylor, J. R. & Stocker, R. Trade-offs of chemotactic foraging in turbulent water. Science 338, 675–679 (2012).

    CAS 
    PubMed 

    Google Scholar 

  • Govern, C. C. & ten Wolde, P. R. Optimal resource allocation in cellular sensing systems. Proc. Natl Acad. Sci. USA 111, 17486–17491 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Sourjik, V. & Berg, H. C. Binding of the Escherichia coli response regulator CheY to its target measured in vivo by fluorescence resonance energy transfer. Proc. Natl Acad. Sci. USA 99, 12669–12674 (2002).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lan, G., Sartori, P., Neumann, S., Sourjik, V. & Tu, Y. The energy–speed–accuracy trade-off in sensory adaptation. Nat. Phys. 8, 422–428 (2012).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Stouthamer, A. H. & Bettenhaussen, C. W. A continuous culture study of an ATPase-negative mutant of Escherichia coli. Arch. Microbiol. 113, 185–189 (1977).

    CAS 
    PubMed 

    Google Scholar 

  • Macnab, R. M. in Escherichia coli and Salmonella Typhimurium: Cellular and Molecular Biology Vol. 1 (eds Nerdhardt, F. et al.) 732–759 (American Society for Microbiology, 1987).

  • Kempes, C. P. et al. Drivers of bacterial maintenance and minimal energy requirements. Front. Microbiol. 8, 31 (2017).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Lynch, M. & Marinov, G. K. The bioenergetic costs of a gene. Proc. Natl Acad. Sci. USA 112, 15690–15695 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hoehler, T. M. & Jørgensen, B. B. Microbial life under extreme energy limitation. Nat. Rev. Microbiol. 11, 83–94 (2013).

    CAS 
    PubMed 

    Google Scholar 

  • Boehm, A. et al. Second messenger-mediated adjustment of bacterial swimming velocity. Cell 141, 107–116 (2010).

    CAS 
    PubMed 

    Google Scholar 

  • Fang, X. & Gomelsky, M. A post-translational, c-di-GMP-dependent mechanism regulating flagellar motility: c-di-GMP-dependent flagellum rotation bias. Mol. Microbiol. 76, 1295–1305 (2010).

    CAS 
    PubMed 

    Google Scholar 

  • Sathyamoorthy, R. et al. To hunt or to rest: prey depletion induces a novel starvation survival strategy in bacterial predators. ISME J. 15, 109–123 (2020).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Adler, J. & Templeton, B. The effect of environmental conditions on the motility of Escherichia coli. J. Gen. Microbiol. 46, 175–184 (1967).

    CAS 
    PubMed 

    Google Scholar 

  • Berg, H. C. & Tedesco, P. M. Transient response to chemotactic stimuli in Escherichia coli. Proc. Natl Acad. Sci. USA 72, 3235–3239 (1975).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mitchell, J. G. The influence of cell size on marine bacterial motility and energetics. Microb. Ecol. 22, 227–238 (1991).

    CAS 
    PubMed 

    Google Scholar 

  • Castro-Sowinski, S., Burdman, S., Matan, O. & Okon, Y. in Plastics from Bacteria Vol. 14 (ed. Chen, G. G.-Q.) 39–61 (Springer, 2010).

  • Walter, J. M., Greenfield, D., Bustamante, C. & Liphardt, J. Light-powering Escherichia coli with proteorhodopsin. Proc. Natl Acad. Sci. USA 104, 2408–2412 (2007).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Gude, S. et al. Bacterial coexistence driven by motility and spatial competition. Nature 578, 588–592 (2020). This work presents evidence for a trade-off between motility and growth, which supports bacterial diversity through spatial segregation.

    CAS 
    PubMed 

    Google Scholar 

  • Ni, B., Colin, R., Link, H., Endres, R. G. & Sourjik, V. Growth-rate dependent resource investment in bacterial motile behavior quantitatively follows potential benefit of chemotaxis. Proc. Natl Acad. Sci. USA 117, 595–601 (2020). This work systematically compares the cost and benefit of chemotaxis in spatially extended and well-mixed environments.

    CAS 
    PubMed 

    Google Scholar 

  • Li, M. & Hazelbauer, G. L. Cellular stoichiometry of the components of the chemotaxis signaling complex. J. Bacteriol. 186, 3687–3694 (2004).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Neumann, S., Hansen, C. H., Wingreen, N. S. & Sourjik, V. Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxis. EMBO J. 29, 3484–3495 (2010).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Akashi, H. & Gojobori, T. Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc. Natl Acad. Sci. USA 99, 3695–3700 (2002).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Basan, M. et al. Overflow metabolism in Escherichia coli results from efficient proteome allocation. Nature 528, 99–104 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ni, B. et al. Evolutionary remodeling of bacterial motility checkpoint control. Cell Rep. 18, 866–877 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Fraebel, D. T. et al. Environment determines evolutionary trajectory in a constrained phenotypic space. eLife 6, e24669 (2017).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Honda, T. et al. Coordination of gene expression with cell size enables Escherichia coli to efficiently maintain motility across conditions. Preprint at bioRxiv https://doi.org/10.1101/2021.05.12.443892 (2021).

    Article 

    Google Scholar 

  • Zampieri, M., Hörl, M., Hotz, F., Müller, N. F. & Sauer, U. Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli. Nat. Commun. 10, 3354 (2019).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Zhao, Z. et al. Frequent pauses in Escherichia coli flagella elongation revealed by single cell real-time fluorescence imaging. Nat. Commun. 9, 1885 (2018).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Zhuang, X. et al. Live‐cell fluorescence imaging reveals dynamic production and loss of bacterial flagella. Mol. Microbiol. 114, 279–291 (2020).

    CAS 
    PubMed 

    Google Scholar 

  • Chevance, F. F. V. & Hughes, K. T. Coordinating assembly of a bacterial macromolecular machine. Nat. Rev. Microbiol. 6, 455–465 (2008). This work presents a classic overview of the gene regulatory pathway that controls flagella assembly in Gram-negative bacteria.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Amsler, C. D., Cho, M. & Matsumura, P. Multiple factors underlying the maximum motility of Escherichia coli as cultures enter post-exponential growth. J. Bacteriol. 175, 6238–6244 (1993).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lopes, J. G. & Sourjik, V. Chemotaxis of Escherichia coli to major hormones and polyamines present in human gut. ISME J. 12, 2736–2747 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Yang, J. et al. Biphasic chemotaxis of Escherichia coli to the microbiota metabolite indole. Proc. Natl Acad. Sci. USA 117, 6114–6120 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Matz, C. & Jürgens, K. High motility reduces grazing mortality of planktonic bacteria. Appl. Environ. Microbiol. 71, 921–929 (2005).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cummings, L. A., Wilkerson, W. D., Bergsbaken, T. & Cookson, B. T. In vivo, fliC expression by Salmonella enterica serovar Typhimurium is heterogeneous, regulated by ClpX, and anatomically restricted. Mol. Microbiol. 61, 795–809 (2006).

    CAS 
    PubMed 

    Google Scholar 

  • Yuan, J. & Berg, H. C. Ultrasensitivity of an adaptive bacterial motor. J. Mol. Biol. 425, 1760–1764 (2013).

    CAS 
    PubMed 

    Google Scholar 

  • Lestas, I., Vinnicombe, G. & Paulsson, J. Fundamental limits on the suppression of molecular fluctuations. Nature 467, 174–178 (2010).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Frankel, N. W. et al. Adaptability of non-genetic diversity in bacterial chemotaxis. eLife 3, e03526 (2014).

    PubMed Central 

    Google Scholar 

  • Goldbeter, A. & Koshland, D. E. An amplified sensitivity arising from covalent modification in biological systems. Proc. Natl Acad. Sci. USA 78, 6840–6844 (1981).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Waite, A. J. et al. Non‐genetic diversity modulates population performance. Mol. Syst. Biol. 12, 895 (2016).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Fu, X. et al. Spatial self-organization resolves conflicts between individuality and collective migration. Nat. Commun. 9, 2177 (2018). This sophisticated microfluidic study reveals that a chemotactic population may travel as a cohesive unit despite strong phenotypic heterogeneity within the population.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Long, Z., Quaife, B., Salman, H. & Oltvai, Z. N. Cell–cell communication enhances bacterial chemotaxis toward external attractants. Sci. Rep. 7, 12855 (2017).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Laganenka, L., Colin, R. & Sourjik, V. Chemotaxis towards autoinducer 2 mediates autoaggregation in Escherichia coli. Nat. Commun. 7, 12984 (2016). This study demonstrates that bacteria may chase self-generated gradients by producing quorum-sensing molecules.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Park, S. et al. Influence of topology on bacterial social interaction. Proc. Natl Acad. Sci. USA 100, 13910–13915 (2003).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Phan, T. V. et al. Bacterial route finding and collective escape in mazes and fractals. Phys. Rev. X 10, 031017 (2020).

    CAS 

    Google Scholar 

  • Waite, A. J., Frankel, N. W. & Emonet, T. Behavioral variability and phenotypic diversity in bacterial chemotaxis. Annu. Rev. Biophys. 47, 595–616 (2018). This work presents a review of the mechanisms underlying behavioural variation in bacterial chemotaxis and the consequences for chemotactic performance.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ackermann, M. A functional perspective on phenotypic heterogeneity in microorganisms. Nat. Rev. Microbiol. 13, 497–508 (2015).

    CAS 
    PubMed 

    Google Scholar 

  • Bódi, Z. et al. Phenotypic heterogeneity promotes adaptive evolution. PLoS Biol. 15, e2000644 (2017).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Seymour, J. R., Amin, S. A., Raina, J.-B. & Stocker, R. Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships. Nat. Microbiol. 2, 17065 (2017).

    CAS 
    PubMed 

    Google Scholar 

  • Weber, L., Gonzalez‐Díaz, P., Armenteros, M. & Apprill, A. The coral ecosphere: a unique coral reef habitat that fosters coral–microbial interactions. Limnol. Oceanogr. 64, 2373–2388 (2019).

    CAS 

    Google Scholar 

  • Salek, M. M., Carrara, F., Fernandez, V., Guasto, J. S. & Stocker, R. Bacterial chemotaxis in a microfluidic T-maze reveals strong phenotypic heterogeneity in chemotactic sensitivity. Nat. Commun. 10, 1877 (2019).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Ford, R. M. & Lauffenburger, D. A. Measurement of bacterial random motility and chemotaxis coefficients: II. Application of single-cell-based mathematical model. Biotechnol. Bioeng. 37, 661–672 (1991).

    CAS 
    PubMed 

    Google Scholar 

  • Lambert, B. S., Fernandez, V. I. & Stocker, R. Motility drives bacterial encounter with particles responsible for carbon export throughout the ocean. Limnol. Oceanogr. Lett. 4, 113–118 (2019).

    Google Scholar 

  • Słomka, J., Alcolombri, U., Secchi, E., Stocker, R. & Fernandez, V. I. Encounter rates between bacteria and small sinking particles. N. J. Phys. 22, 043016 (2020).

    Google Scholar 

  • Hein, A. M. & Martin, B. T. Information limitation and the dynamics of coupled ecological systems. Nat. Ecol. Evol. 4, 82–90 (2020).

    PubMed 

    Google Scholar 

  • Kiorboe, T., Grossart, H.-P., Ploug, H. & Tang, K. Mechanisms and rates of bacterial colonization of sinking aggregates. Appl. Environ. Microbiol. 68, 3996–4006 (2002).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Viswanathan, G. M. et al. Optimizing the success of random searches. Nature 401, 911–914 (1999).

    CAS 
    PubMed 

    Google Scholar 

  • Korobkova, E., Emonet, T., Vilar, J. M. G., Shimizu, T. S. & Cluzel, P. From molecular noise to behavioural variability in a single bacterium. Nature 428, 574–578 (2004).

    CAS 
    PubMed 

    Google Scholar 

  • Tu, Y. & Grinstein, G. How white noise generates power-law switching in bacterial flagellar motors. Phys. Rev. Lett. 4, 208101 (2005).

    Google Scholar 

  • Huo, H., He, R., Zhang, R. & Yuan, J. Swimming Escherichia coli explore the environment by Lévy walk. Appl. Environ. Microbiol. 87, e02429–20 (2021).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Keegstra, J. M. et al. Phenotypic diversity and temporal variability in a bacterial signaling network revealed by single-cell FRET. eLife 6, e27455 (2017).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Colin, R. & Sourjik, V. Multiple sources of slow activity fluctuations in a bacterial chemosensory network. eLife 6, e26796 (2017).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Karin, O. & Alon, U. Temporal fluctuations in chemotaxis gain implements a simulated tempering strategy for efficient navigation in complex environments. SSRN Electron. J. 24, 102796 (2021).

    CAS 

    Google Scholar 

  • Carey, J. N. et al. Regulated stochasticity in a bacterial signaling network permits tolerance to a rapid environmental change. Cell 173, 196–207.e14 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kamino, K., Keegstra, J. M., Long, J., Emonet, T. & Shimizu, T. S. Adaptive tuning of cell sensory diversity without changes in gene expression. Sci. Adv. 6, eabc1087 (2020). This study shows that a bacterial population increases chemotactic bed-hedging when environmental signals are unavailable, but suppresses the sensory diversity when a traceable signal is presented.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bassler, B. L. & Losick, R. Bacterially speaking. Cell 125, 237–246 (2006).

    CAS 
    PubMed 

    Google Scholar 

  • Mukherjee, S. & Bassler, B. L. Bacterial quorum sensing in complex and dynamically changing environments. Nat. Rev. Microbiol. 17, 371–382 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Budrene, E. O. & Berg, H. C. Dynamics of formation of symmetrical patterns by chemotactic bacteria. Nature 376, 49–53 (1995).

    CAS 
    PubMed 

    Google Scholar 

  • Ben-Jacob, E., Cohen, I. & Levine, H. Cooperative self-organization of microorganisms. Adv. Phys. 49, 395–554 (2000).

    CAS 

    Google Scholar 

  • Adler, J. Chemotaxis in bacteria. Science 153, 708–716 (1966).

    CAS 
    PubMed 

    Google Scholar 

  • Keller, E. F. & Segel, L. A. Model for chemotaxis. J. Theor. Biol. 30, 225–234 (1971).

    CAS 
    PubMed 

    Google Scholar 

  • Saragosti, J. et al. Directional persistence of chemotactic bacteria in a traveling concentration wave. Proc. Natl Acad. Sci. USA 108, 16235–16240 (2011).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mattingly & Emonet, T. The balancing act of growth and expansion. Nature 575, 602–603 (2019).

    CAS 
    PubMed 

    Google Scholar 

  • Liu, W., Cremer, J., Li, D., Hwa, T. & Liu, C. An evolutionarily stable strategy to colonize spatially extended habitats. Nature 575, 664–668 (2019). This study reveals that chemotactic strains selected for different speeds of range expansion in semi-solid agar can stably coexist.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hui, S. et al. Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria. Mol. Syst. Biol. 11, 784 (2015).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Maser, A., Peebo, K., Vilu, R. & Nahku, R. Amino acids are key substrates to Escherichia coli BW25113 for achieving high specific growth rate. Res. Microbiol. 171, 185–193 (2020).

    CAS 
    PubMed 

    Google Scholar 

  • Yang, Y. et al. Relation between chemotaxis and consumption of amino acids in bacteria. Mol. Microbiol. 96, 1272–1282 (2015). This study is a pioneering work on the relation between chemotaxis and metabolism, where the relationship between amino acid uptake preference and chemotactic affinity in E. coli and B. subtilis is studied.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cadotte, M. W. et al. On testing the competition–colonization trade-off in a multispecies assemblage. Am. Nat. 168, 704–709 (2006).

    PubMed 

    Google Scholar 

  • Amarasekare, P. Competitive coexistence in spatially structured environments: a synthesis. Ecol. Lett. 6, 1109–1122 (2003).

    Google Scholar 

  • Levins, R. & Culver, D. Regional coexistence of species and competition between rare species. Proc. Natl Acad. Sci. USA 68, 1246–1248 (1971).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Yawata, Y. et al. Competition–dispersal tradeoff ecologically differentiates recently speciated marine bacterioplankton populations. Proc. Natl Acad. Sci. USA 111, 5622–5627 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Narla, A. V., Cremer, J. & Hwa, T. A traveling-wave solution for bacterial chemotaxis with growth. Proc. Natl Acad. Sci. USA 118, e2105138118 (2021). This work develops a comprehensive mathematical framework describing migrating bands of bacteria driven by growth and chemotaxis that is applicable to many environments.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bassler, B. L., Gibbons, P. J., Yu, C. & Roseman, S. Chemotaxis to chitin oligosaccharides by Vibrio furnissi. J. Biol. Chem. 266, 24268–24275 (1991).

    CAS 
    PubMed 

    Google Scholar 

  • Konishi, H., Hio, M., Kobayashi, M., Takase, R. & Hashimoto, W. Bacterial chemotaxis towards polysaccharide pectin by pectin-binding protein. Sci. Rep. 10, 3977 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Alcolombri, U. et al. Sinking enhances the degradation of organic particles by marine bacteria. Nat. Geosci. 14, 775–780 (2021).

    CAS 

    Google Scholar 

  • D’Souza, G. G., Povolo, V. R., Keegstra, J. M., Stocker, R. & Ackermann, M. Nutrient complexity triggers transitions between solitary and colonial growth in bacterial populations. ISME J. 1, 1 (2021).

    Google Scholar 

  • Nesper, J. et al. Cyclic di-GMP differentially tunes a bacterial flagellar motor through a novel class of CheY-like regulators. eLife 6, e28842 (2017).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Basan, M. et al. A universal trade-off between growth and lag in fluctuating environments. Nature 584, 470–474 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Nguyen, J. et al. A distinct growth physiology enhances bacterial growth under rapid nutrient fluctuations. Nat. Commun. 12, 3662 (2021).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Costello, E. K., Stagaman, K., Dethlefsen, L., Bohannan, B. J. M. & Relman, D. A. The application of ecological theory toward an understanding of the human microbiome. Science 336, 1255–1262 (2012).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cordero, O. X. & Datta, M. S. Microbial interactions and community assembly at microscales. Curr. Opin. Microbiol. 31, 227–234 (2016).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Rusconi, R., Garren, M. & Stocker, R. Microfluidics expanding the frontiers of microbial ecology. Annu. Rev. Biophys. 43, 65–91 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lambert, B. S. et al. A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities. Nat. Microbiol. 2, 1344–1349 (2017).

    CAS 
    PubMed 

    Google Scholar 

  • Clerc, E. E., Raina, J.-B., Lambert, B. S., Seymour, J. & Stocker, R. In situ chemotaxis assay to examine microbial behavior in aquatic ecosystems. J. Vis. Exp. 159, e61062 (2020).

    Google Scholar 

  • Pleška, M., Jordan, D., Frentz, Z., Xue, B. & Leibler, S. Nongenetic individuality, changeability, and inheritance in bacterial behavior. Proc. Natl Acad. Sci. USA 118, e2023322118 (2021).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Figueroa-Morales, N. et al. 3D spatial exploration by E. coli echoes motor temporal variability. Phys. Rev. X 10, 021004 (2020).

    CAS 

    Google Scholar 

  • Hazelbauer, G. L. Bacterial chemotaxis: the early years of molecular studies. Annu. Rev. Microbiol. 66, 285–303 (2012).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Adler, J., Hazelbauer, G. L. & Dahl, M. M. Chemotaxis toward sugars in Escherichia coli. J. Bacteriol. 115, 824–847 (1973).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mesibov, R. & Adler, J. Chemotaxis toward amino acids in Escherichia coli. J. Bacteriol. 112, 12 (1972).

    Google Scholar 

  • Dekel, E. & Alon, U. Optimality and evolutionary tuning of the expression level of a protein. Nature 436, 588–592 (2005).

    CAS 
    PubMed 

    Google Scholar 

  • Erickson, D. W. et al. A global resource allocation strategy governs growth transition kinetics of Escherichia coli. Nature 551, 119–123 (2017).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Berg, H. C. & Purcell, E. M. Physics of chemoreception. Biophys. J. 20, 193–219 (1977).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mora, T. & Wingreen, N. S. Limits of sensing temporal concentration changes by single cells. Phys. Rev. Lett. 104, 248101 (2010).

    PubMed 

    Google Scholar 

  • Brumley, D. R. et al. Bacteria push the limits of chemotactic precision to navigate dynamic chemical gradients. Proc. Natl Acad. Sci. USA 116, 10792–10797 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mattingly, H. H., Kamino, K., Machta, B. B. & Emonet, T. Escherichia coli chemotaxis is information limited. Nat. Phys. 17, 1426–1431 (2021).

    CAS 
    PubMed 

    Google Scholar 

  • Clausznitzer, D., Micali, G., Neumann, S., Sourjik, V. & Endres, R. G. Predicting chemical environments of bacteria from receptor signaling. PLoS Comput. Biol. 10, e1003870 (2014).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Flores, M., Shimizu, T. S., ten Wolde, P. R. & Tostevin, F. Signaling noise enhances chemotactic drift of E. coli. Phys. Rev. Lett. 109, 148101 (2012).

    PubMed 

    Google Scholar 

  • Okubo, A. & Levin, S. A. Diffusion and Ecological Problems: Modern Perspectives Vol. 14 (Springer, 2001).

  • Fisher, R. A. The wave of advance of advantageous genes. Ann. Eugen. 7, 355–369 (1937).

    Google Scholar 

  • Kolmogorov, A., Petrovskii, I. & Piskunov, N. Study of a diffusion equation that is related to the growth of a quality of matter and its application to a biological problem. Mosc. Univ. Math. Bull. 1, 1–26 (1937).

    Google Scholar 

  • Giometto, A., Rinaldo, A., Carrara, F. & Altermatt, F. Emerging predictable features of replicated biological invasion fronts. Proc. Natl Acad. Sci. USA 111, 297–301 (2014).

    CAS 
    PubMed 

    Google Scholar 

  • Gandhi, S. R., Yurtsev, E. A., Korolev, K. S. & Gore, J. Range expansions transition from pulled to pushed waves as growth becomes more cooperative in an experimental microbial population. Proc. Natl Acad. Sci. USA 113, 6922–6927 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Painter, K. J. Mathematical models for chemotaxis and their applications in self-organisation phenomena. J. Theor. Biol. 481, 162–182 (2019).

    PubMed 

    Google Scholar 


  • Source: Ecology - nature.com

    Microbes and minerals may have set off Earth’s oxygenation

    Caller ID for Risso’s and Pacific White-sided dolphins