Hydrodynamics and collective behavior of the tethered bacterium<i>Thiovulum majus</i>

Petroff, Alexander P.; Libchaber, Albert

doi:10.1073/pnas.1322092111

Cited by 29 publications

(38 citation statements)

References 40 publications

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“…Both T. majus and Uronemella cells were collected from the sulfidic mud of a salt marsh in Woods Hole, MA (40°31′33.34′′ N, 70°40′6.19′′ W). The techniques used to enrich these cells are nearly identical and have been previously described [ 16 , 29 ]. Inspection of water taken from pore spaces in this mud initially revealed an abundance of both T. majus and Uronemella living within the same samples.…”

Section: Methodsmentioning

confidence: 99%

“…[ 14 , 15 ] ( figure 2 ). These microbes have separately evolved the ability to form communities that generate large-scale fluid flows which transport oxygen to cells forty times faster than diffusion [ 9 , 16 ]. To do so, cells first accumulate into a band at a particular oxygen concentration [ 17 , 18 ].…”

Section: Introductionmentioning

confidence: 99%

“…When cells are uniformly distributed on a sheet, they only stir their environment on the scale of a cell. Attachment and detachment of cells from the veil generate millimetre-scale density fluctuations [ 16 , 23 , 24 ] that produce a large-scale convective flow [ 9 , 16 , 22 ].…”

Section: Introductionmentioning

confidence: 99%

“…Here, we combine past observations with new experiments and analysis to highlight how the similar collective dynamics displayed by these veil-forming microbes arise from the behaviours of individual cells to mitigate diffusion limitation. The formation of a veil and the generation of a large-scale flow are consequences of the traits microbes evolved to position themselves in a nutrient gradient, attach to a surface, and individually generate a flow of oxygen-rich water [ 16 ]. We identify three evolutionary innovations that allow cells to form veils.…”

Section: Introductionmentioning

confidence: 99%

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Biophysical basis for convergent evolution of two veil-forming microbes

et al. 2015

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Microbes living in stagnant water typically rely on chemical diffusion to draw nutrients from their environment. The sulfur-oxidizing bacterium Thiovulum majus and the ciliate Uronemella have independently evolved the ability to form a ‘veil’, a centimetre-scale mucous sheet on which cells organize to produce a macroscopic flow. This flow pulls nutrients through the community an order of magnitude faster than diffusion. To understand how natural selection led these microbes to evolve this collective behaviour, we connect the physical limitations acting on individual cells to the cell traits. We show how diffusion limitation and viscous dissipation have led individual T. majus and Uronemella cells to display two similar characteristics. Both of these cells exert a force of approximately 40 pN on the water and attach to boundaries by means of a mucous stalk. We show how the diffusion coefficient of oxygen in water and the viscosity of water define the force the cells must exert. We then show how the hydrodynamics of filter-feeding orient a microbe normal to the surface to which it attaches. Finally, we combine these results with new observations of veil formation and a review of veil dynamics to compare the collective dynamics of these microbes. We conclude that this convergent evolution is a reflection of similar physical limitations imposed by diffusion and viscosity acting on individual cells.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Biophysical basis for convergent evolution of two veil-forming microbes

et al. 2015

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“…As a consequence, membranes tend to develop into shapes that are far from that of a sphere (Harris and Theriot, ). Subsequently, shapes, and odd shapes in particular, will open the door for novel functions, for example , see Thiovulum majus which uses an unusual hydrodynamic power to get the environmental water medium to approach the cell and feed it (Petroff and Libchaber, ).…”

Section: Statistical Approachesmentioning

confidence: 99%

No wisdom in the crowd: genome annotation in the era of big data – current status and future prospects

Danchin

Ouzounis

Tokuyasu

et al. 2018

Microbial Biotechnology

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SummaryScience and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery‐driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential in biological research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from ‘the sequence tells the structure tells the function’ fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader.

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