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Kiørboe T. Predation in a Microbial World: Mechanisms and Trade-Offs of Flagellate Foraging. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:361-381. [PMID: 37368955 DOI: 10.1146/annurev-marine-020123-102001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Heterotrophic nanoflagellates are the main consumers of bacteria and picophytoplankton in the ocean and thus play a key role in ocean biogeochemistry. They are found in all major branches of the eukaryotic tree of life but are united by all being equipped with one or a few flagella that they use to generate a feeding current. These microbial predators are faced with the challenges that viscosity at this small scale impedes predator-prey contact and that their foraging activity disturbs the ambient water and thus attracts their own flow-sensing predators. Here, I describe some of the diverse adaptations of the flagellum to produce sufficient force to overcome viscosity and of the flagellar arrangement to minimize fluid disturbances, and thus of the various solutions to optimize the foraging-predation risk trade-off. I demonstrate how insights into this trade-off can be used to develop robust trait-based models of microbial food webs.
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Affiliation(s)
- Thomas Kiørboe
- Centre for Ocean Life, DTU Aqua, Technical University of Denmark, Kongens Lyngby, Denmark;
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2
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Seymour JR, Brumley DR, Stocker R, Raina JB. Swimming towards each other: the role of chemotaxis in bacterial interactions. Trends Microbiol 2024:S0966-842X(23)00360-8. [PMID: 38212193 DOI: 10.1016/j.tim.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/13/2024]
Abstract
Chemotaxis allows microorganisms to direct movement in response to chemical stimuli. Bacteria use this behaviour to develop spatial associations with animals and plants, and even larger microbes. However, current theory suggests that constraints imposed by the limits of chemotactic sensory systems will prevent sensing of chemical gradients emanating from cells smaller than a few micrometres, precluding the utility of chemotaxis in interactions between individual bacteria. Yet, recent evidence has revealed surprising levels of bacterial chemotactic precision, as well as a role for chemotaxis in metabolite exchange between bacterial cells. If indeed widespread, chemotactic sensing between bacteria could represent an important, but largely overlooked, phenotype within interbacterial interactions, and play a significant role in shaping cooperative and competitive relationships.
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Affiliation(s)
- Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Broadway, New South Wales, Australia.
| | - Douglas R Brumley
- School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia.
| | - Roman Stocker
- Institute for Environmental Engineering, Department of Civil, Environmental, and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Broadway, New South Wales, Australia.
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3
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Noell SE, Brennan E, Washburn Q, Davis EW, Hellweger FL, Giovannoni SJ. Differences in the regulatory strategies of marine oligotrophs and copiotrophs reflect differences in motility. Environ Microbiol 2023. [PMID: 36826469 DOI: 10.1111/1462-2920.16357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/22/2023] [Indexed: 02/25/2023]
Abstract
Aquatic bacteria frequently are divided into lifestyle categories oligotroph or copiotroph. Oligotrophs have proportionately fewer transcriptional regulatory genes than copiotrophs and are generally non-motile/chemotactic. We hypothesized that the absence of chemotaxis/motility in oligotrophs prevents them from occupying nutrient patches long enough to benefit from transcriptional regulation. We first confirmed that marine oligotrophs are generally reduced in genes for transcriptional regulation and motility/chemotaxis. Next, using a non-motile oligotroph (Ca. Pelagibacter st. HTCC7211), a motile copiotroph (Alteromonas macleodii st. HOT1A3), and [14 C]l-alanine, we confirmed that l-alanine catabolism is not transcriptionally regulated in HTCC7211 but is in HOT1A3. We then found that HOT1A3 took 2.5-4 min to initiate l-alanine oxidation at patch l-alanine concentrations, compared to <30 s for HTCC7211. By modelling cell trajectories, we predicted that, in most scenarios, non-motile cells spend <2 min in patches, compared to >4 min for chemotactic/motile cells. Thus, the time necessary for transcriptional regulation to initiate prevents transcriptional regulation from being beneficial for non-motile oligotrophs. This is supported by a mechanistic model we developed, which predicted that HTCC7211 cells with transcriptional regulation of l-alanine metabolism would produce 12% of their standing ATP stock upon encountering an l-alanine patch, compared to 880% in HTCC7211 cells without transcriptional regulation.
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Affiliation(s)
- Stephen E Noell
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Elizabeth Brennan
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Quinn Washburn
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Edward W Davis
- Center for Quantitative Life Sciences, Oregon State University, Oregon, USA
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4
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Zhao G, He H, Wang H, Liang Y, Guo C, Shao H, Jiang Y, Wang M. Variations in Marine Bacterial and Archaeal Communities during an Ulva prolifera Green Tide in Coastal Qingdao Areas. Microorganisms 2022; 10:microorganisms10061204. [PMID: 35744722 PMCID: PMC9228619 DOI: 10.3390/microorganisms10061204] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 11/23/2022] Open
Abstract
Green tides caused by Ulva prolifera occur annually in the Yellow Sea, potentially influencing the marine microorganisms. Here, we focused on the variations in marine bacterial and archaeal communities during an U. prolifera green tide in coastal Qingdao areas with Illumina high-throughput sequencing analysis. Our results revealed that the diversity and structure of bacterial and archaeal communities, as well as the organization and structure of microbial co-occurrence networks, varied during the green tide. The decline phase may be favorable to the bacterial and archaeal diversity and richness. The bacterial community, as well as the archaeal community, showed clear variations between the outbreak and decline phases. A simpler and less connected microbial co-occurrence network was observed during the outbreak phase compared with the decline phase. Flavobacteriales and Rhodobacterales separately dominated the bacterial community during the outbreak and decline phase, and Marine Group II (MGII) dominated the archaeal community during the green tide. Combined with microbial co-occurrence network analysis, Flavobacteriales, Rhodobacterales and MGII may be important organisms during the green tide. Temperature, chlorophyll a content and salinity may have an important impact on the variations in bacterial and archaeal communities during the green tide.
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Affiliation(s)
- Guihua Zhao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
| | - Hui He
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
- Correspondence: (H.H.); (M.W.)
| | - Hualong Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
| | - Cui Guo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
| | - Yong Jiang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; (G.Z.); (H.W.); (Y.L.); (C.G.); (H.S.); (Y.J.)
- The Affiliated Hospital of Qingdao University, Qingdao 266000, China
- OUC-UMT Joint Academic Centre for Marine Studies, Qingdao 266003, China
- Correspondence: (H.H.); (M.W.)
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5
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Gao C, Garren M, Penn K, Fernandez VI, Seymour JR, Thompson JR, Raina JB, Stocker R. Coral mucus rapidly induces chemokinesis and genome-wide transcriptional shifts toward early pathogenesis in a bacterial coral pathogen. THE ISME JOURNAL 2021; 15:3668-3682. [PMID: 34168314 PMCID: PMC8630044 DOI: 10.1038/s41396-021-01024-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/12/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023]
Abstract
Elevated seawater temperatures have contributed to the rise of coral disease mediated by bacterial pathogens, such as the globally distributed Vibrio coralliilyticus, which utilizes coral mucus as a chemical cue to locate stressed corals. However, the physiological events in the pathogens that follow their entry into the coral host environment remain unknown. Here, we present simultaneous measurements of the behavioral and transcriptional responses of V. coralliilyticus BAA-450 incubated in coral mucus. Video microscopy revealed a strong and rapid chemokinetic behavioral response by the pathogen, characterized by a two-fold increase in average swimming speed within 6 min of coral mucus exposure. RNA sequencing showed that this bacterial behavior was accompanied by an equally rapid differential expression of 53% of the genes in the V. coralliilyticus genome. Specifically, transcript abundance 10 min after mucus exposure showed upregulation of genes involved in quorum sensing, biofilm formation, and nutrient metabolism, and downregulation of flagella synthesis and chemotaxis genes. After 60 min, we observed upregulation of genes associated with virulence, including zinc metalloproteases responsible for causing coral tissue damage and algal symbiont photoinactivation, and secretion systems that may export toxins. Together, our results suggest that V. coralliilyticus employs a suite of behavioral and transcriptional responses to rapidly shift into a distinct infection mode within minutes of exposure to the coral microenvironment.
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Affiliation(s)
- Cherry Gao
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Civil and Environmental Engineering, Ralph M. Parsons Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
| | - Melissa Garren
- Working Ocean Strategies LLC, Carmel, CA, USA
- Department of Applied Environmental Science, California State University Monterey Bay, Seaside, CA, USA
| | - Kevin Penn
- Department of Civil and Environmental Engineering, Ralph M. Parsons Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Vicente I Fernandez
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
| | - Justin R Seymour
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | - Janelle R Thompson
- Singapore Center for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | - Jean-Baptiste Raina
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland.
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6
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Foraging trade-offs, flagellar arrangements, and flow architecture of planktonic protists. Proc Natl Acad Sci U S A 2021; 118:2009930118. [PMID: 33431666 DOI: 10.1073/pnas.2009930118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Unicellular flagellated protists are a key element in aquatic microbial food webs. They all use flagella to swim and to generate feeding currents to encounter prey and enhance nutrient uptake. At the same time, the beating flagella create flow disturbances that attract flow-sensing predators. Protists have highly diverse flagellar arrangements in terms of number of flagella and their position, beat pattern, and kinematics, but it is unclear how the various arrangements optimize the fundamental trade-off between resource acquisition and predation risk. Here we describe the near-cell flow fields produced by 15 species and demonstrate consistent relationships between flagellar arrangement and swimming speed and between flagellar arrangement and flow architecture, and a trade-off between resource acquisition and predation risk. The flow fields fall in categories that are qualitatively described by simple point force models that include the drag force of the moving cell body and the propulsive forces of the flagella. The trade-off between resource acquisition and predation risk varies characteristically between flow architectures: Flagellates with multiple flagella have higher predation risk relative to their clearance rate compared to species with only one active flagellum, with the exception of the highly successful dinoflagellates that have simultaneously achieved high clearance rates and stealth behavior due to a unique flagellar arrangement. Microbial communities are shaped by trade-offs and environmental constraints, and a mechanistic explanation of foraging trade-offs is a vital part of understanding the eukaryotic communities that form the basis of pelagic food webs.
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7
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Distinct nitrogen cycling and steep chemical gradients in Trichodesmium colonies. ISME JOURNAL 2019; 14:399-412. [PMID: 31636364 PMCID: PMC6976679 DOI: 10.1038/s41396-019-0514-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 09/10/2019] [Accepted: 09/11/2019] [Indexed: 11/08/2022]
Abstract
Trichodesmium is an important dinitrogen (N2)-fixing cyanobacterium in marine ecosystems. Recent nucleic acid analyses indicate that Trichodesmium colonies with their diverse epibionts support various nitrogen (N) transformations beyond N2 fixation. However, rates of these transformations and concentration gradients of N compounds in Trichodesmium colonies remain largely unresolved. We combined isotope-tracer incubations, micro-profiling and numeric modelling to explore carbon fixation, N cycling processes as well as oxygen, ammonium and nitrate concentration gradients in individual field-sampled Trichodesmium colonies. Colonies were net-autotrophic, with carbon and N2 fixation occurring mostly during the day. Ten percent of the fixed N was released as ammonium after 12-h incubations. Nitrification was not detectable but nitrate consumption was high when nitrate was added. The consumed nitrate was partly reduced to ammonium, while denitrification was insignificant. Thus, the potential N transformation network was characterised by fixed N gain and recycling processes rather than denitrification. Oxygen concentrations within colonies were ~60-200% air-saturation. Moreover, our modelling predicted steep concentration gradients, with up to 6-fold higher ammonium concentrations, and nitrate depletion in the colony centre compared to the ambient seawater. These gradients created a chemically heterogeneous microenvironment, presumably facilitating diverse microbial metabolisms in millimetre-sized Trichodesmium colonies.
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8
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Bondoc KGV, Lembke C, Lang SN, Germerodt S, Schuster S, Vyverman W, Pohnert G. Decision-making of the benthic diatom Seminavis robusta searching for inorganic nutrients and pheromones. ISME JOURNAL 2018; 13:537-546. [PMID: 30301945 PMCID: PMC6331598 DOI: 10.1038/s41396-018-0299-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 09/12/2018] [Accepted: 09/14/2018] [Indexed: 11/28/2022]
Abstract
Microorganisms encounter a diversity of chemical stimuli that trigger individual responses and influence population dynamics. However, microbial behavior under the influence of different incentives and microbial decision-making is poorly understood. Benthic marine diatoms that react to sexual attractants as well as to nutrient gradients face such multiple constraints. Here, we document and model behavioral complexity and context-sensitive responses of these motile unicellular algae to sex pheromones and the nutrient silicate. Throughout the life cycle of the model diatom Seminavis robusta nutrient-starved cells localize sources of silicate by combined chemokinetic and chemotactic motility. However, with an increasing need for sex to restore the initial cell size, a change in behavior favoring the attraction-pheromone-guided search for a mating partner takes place. When sex becomes inevitable to prevent cell death, safeguard mechanisms are abandoned, and cells prioritize the search for mating partners. Such selection processes help to explain biofilm organization and to understand species interactions in complex communities.
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Affiliation(s)
- Karen Grace V Bondoc
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Lessingstrasse 8, D-07743, Jena, Germany. .,Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, D-07745, Jena, Germany. .,Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901-8521, USA.
| | - Christine Lembke
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Lessingstrasse 8, D-07743, Jena, Germany.,Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, D-16775, Stechlin, Germany
| | - Stefan N Lang
- Department of Bioinformatics, Friedrich-Schiller-Universität Jena, Ernst-Abbe-Platz 2, D-07743, Jena, Germany
| | - Sebastian Germerodt
- Department of Bioinformatics, Friedrich-Schiller-Universität Jena, Ernst-Abbe-Platz 2, D-07743, Jena, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Friedrich-Schiller-Universität Jena, Ernst-Abbe-Platz 2, D-07743, Jena, Germany
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Gent, Krijgslaan 281 S8, 9000, Gent, Belgium
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Lessingstrasse 8, D-07743, Jena, Germany. .,Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, D-07745, Jena, Germany.
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9
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Nagy K, Ábrahám Á, Keymer JE, Galajda P. Application of Microfluidics in Experimental Ecology: The Importance of Being Spatial. Front Microbiol 2018; 9:496. [PMID: 29616009 PMCID: PMC5870036 DOI: 10.3389/fmicb.2018.00496] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/02/2018] [Indexed: 12/21/2022] Open
Abstract
Microfluidics is an emerging technology that is used more and more in biology experiments. Its capabilities of creating precisely controlled conditions in cellular dimensions make it ideal to explore cell-cell and cell-environment interactions. Thus, a wide spectrum of problems in microbial ecology can be studied using engineered microbial habitats. Moreover, artificial microfluidic ecosystems can serve as model systems to test ecology theories and principles that apply on a higher level in the hierarchy of biological organization. In this mini review we aim to demonstrate the versatility of microfluidics and the diversity of its applications that help the advance of microbiology, and in more general, experimental ecology.
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Affiliation(s)
- Krisztina Nagy
- Biological Research Centre, Institute of Biophysics, Hungarian Academy of Sciences, Szeged, Hungary
| | - Ágnes Ábrahám
- Biological Research Centre, Institute of Biophysics, Hungarian Academy of Sciences, Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged, Hungary
| | - Juan E. Keymer
- School of Biological Sciences and School of Physics, Pontifical Catholic University of Chile, Santiago, Chile
| | - Péter Galajda
- Biological Research Centre, Institute of Biophysics, Hungarian Academy of Sciences, Szeged, Hungary
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10
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Jashnsaz H, Anderson GG, Pressé S. Statistical signatures of a targeted search by bacteria. Phys Biol 2017; 14:065002. [PMID: 28809162 DOI: 10.1088/1478-3975/aa84ea] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Chemoattractant gradients are rarely well-controlled in nature and recent attention has turned to bacterial chemotaxis toward typical bacterial food sources such as food patches or even bacterial prey. In environments with localized food sources reminiscent of a bacterium's natural habitat, striking phenomena-such as the volcano effect or banding-have been predicted or expected to emerge from chemotactic models. However, in practice, from limited bacterial trajectory data it is difficult to distinguish targeted searches from an untargeted search strategy for food sources. Here we use a theoretical model to identify statistical signatures of a targeted search toward point food sources, such as prey. Our model is constructed on the basis that bacteria use temporal comparisons to bias their random walk, exhibit finite memory and are subject to random (Brownian) motion as well as signaling noise. The advantage with using a stochastic model-based approach is that a stochastic model may be parametrized from individual stochastic bacterial trajectories but may then be used to generate a very large number of simulated trajectories to explore average behaviors obtained from stochastic search strategies. For example, our model predicts that a bacterium's diffusion coefficient increases as it approaches the point source and that, in the presence of multiple sources, bacteria may take substantially longer to locate their first source giving the impression of an untargeted search strategy.
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Affiliation(s)
- Hossein Jashnsaz
- Department of Physics, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, IN 46202, United States of America
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11
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Walsh EJ, Feuerborn A, Wheeler JHR, Tan AN, Durham WM, Foster KR, Cook PR. Microfluidics with fluid walls. Nat Commun 2017; 8:816. [PMID: 29018186 PMCID: PMC5635017 DOI: 10.1038/s41467-017-00846-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/28/2017] [Indexed: 11/09/2022] Open
Abstract
Microfluidics has great potential, but the complexity of fabricating and operating devices has limited its use. Here we describe a method - Freestyle Fluidics - that overcomes many key limitations. In this method, liquids are confined by fluid (not solid) walls. Aqueous circuits with any 2D shape are printed in seconds on plastic or glass Petri dishes; then, interfacial forces pin liquids to substrates, and overlaying an immiscible liquid prevents evaporation. Confining fluid walls are pliant and resilient; they self-heal when liquids are pipetted through them. We drive flow through a wide range of circuits passively by manipulating surface tension and hydrostatic pressure, and actively using external pumps. Finally, we validate the technology with two challenging applications - triggering an inflammatory response in human cells and chemotaxis in bacterial biofilms. This approach provides a powerful and versatile alternative to traditional microfluidics.The complexity of fabricating and operating microfluidic devices limits their use. Walsh et al. describe a method in which circuits are printed as quickly and simply as writing with a pen, and liquids in them are confined by fluid instead of solid walls.
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Affiliation(s)
- Edmond J Walsh
- Department of Engineering Science, Osney Thermo-Fluids Laboratory, University of Oxford, Osney Mead, Oxford, OX2 0ES, UK.
| | - Alexander Feuerborn
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - James H R Wheeler
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Ann Na Tan
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - William M Durham
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.,Department of Physics and Astronomy, University of Sheffield, Hounsfield Road, Sheffield, S3 7RH, UK
| | - Kevin R Foster
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Peter R Cook
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
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12
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Shang W, Tsao CY, Luo X, Teodoro M, McKay R, Quan DN, Wu HC, Payne GF, Bentley WE. A simple and reusable bilayer membrane-based microfluidic device for the study of gradient-mediated bacterial behaviors. BIOMICROFLUIDICS 2017; 11:044114. [PMID: 28868107 PMCID: PMC5566557 DOI: 10.1063/1.4993438] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/10/2017] [Indexed: 05/11/2023]
Abstract
We have developed a user-friendly microfluidic device for the study of gradient-mediated bacterial behaviors, including chemotaxis. This device rapidly establishes linear concentration gradients by exploiting solute diffusion through porous membranes in the absence of convective flows. As such, the gradients are created rapidly and can be sustained for long time periods (e.g., hours), sufficient to evaluate cell phenotype. The device exploits a unique simple bilayer configuration that enables rapid setup and quick reproducible introduction of cells. Its reusability represents an additional advantage in that it need not be limited to settings with microfluidics expertise. We have successfully demonstrated the applicability of this tool in studying the chemotactic response of Escherichia coli to glucose. When coupled with our recent Python program, quantified metrics such as speed, ratio of tumble to run, and effective diffusivity can be obtained from slow frame rate videos. Moreover, we introduce a chemotaxis partition coefficient that conveniently scores swimming behavior on the single-cell level.
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Affiliation(s)
| | | | - Xiaolong Luo
- Department of Mechanical Engineering, The Catholic University of America, Washington, 20064, USA
| | | | | | | | - Hsuan-Chen Wu
- Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
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13
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Seymour JR, Amin SA, Raina JB, Stocker R. Zooming in on the phycosphere: the ecological interface for phytoplankton-bacteria relationships. Nat Microbiol 2017; 2:17065. [PMID: 28555622 DOI: 10.1038/nmicrobiol.2017.65] [Citation(s) in RCA: 460] [Impact Index Per Article: 65.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 03/23/2017] [Indexed: 12/28/2022]
Abstract
By controlling nutrient cycling and biomass production at the base of the food web, interactions between phytoplankton and bacteria represent a fundamental ecological relationship in aquatic environments. Although typically studied over large spatiotemporal scales, emerging evidence indicates that this relationship is often governed by microscale interactions played out within the region immediately surrounding individual phytoplankton cells. This microenvironment, known as the phycosphere, is the planktonic analogue of the rhizosphere in plants. The exchange of metabolites and infochemicals at this interface governs phytoplankton-bacteria relationships, which span mutualism, commensalism, antagonism, parasitism and competition. The importance of the phycosphere has been postulated for four decades, yet only recently have new technological and conceptual frameworks made it possible to start teasing apart the complex nature of this unique microbial habitat. It has subsequently become apparent that the chemical exchanges and ecological interactions between phytoplankton and bacteria are far more sophisticated than previously thought and often require close proximity of the two partners, which is facilitated by bacterial colonization of the phycosphere. It is also becoming increasingly clear that while interactions taking place within the phycosphere occur at the scale of individual microorganisms, they exert an ecosystem-scale influence on fundamental processes including nutrient provision and regeneration, primary production, toxin biosynthesis and biogeochemical cycling. Here we review the fundamental physical, chemical and ecological features of the phycosphere, with the goal of delivering a fresh perspective on the nature and importance of phytoplankton-bacteria interactions in aquatic ecosystems.
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Affiliation(s)
- Justin R Seymour
- Climate Change Cluster (C3), University of Technology Sydney, New South Wales 2007, Australia
| | - Shady A Amin
- Department of Biology, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates.,Department of Chemistry, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Jean-Baptiste Raina
- Climate Change Cluster (C3), University of Technology Sydney, New South Wales 2007, Australia
| | - Roman Stocker
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Stefano-Franscini-Platz 5, 8093 Zurich, Switzerland
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14
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Hein AM, Brumley DR, Carrara F, Stocker R, Levin SA. Physical limits on bacterial navigation in dynamic environments. J R Soc Interface 2016; 13:20150844. [PMID: 26763331 DOI: 10.1098/rsif.2015.0844] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Many chemotactic bacteria inhabit environments in which chemicals appear as localized pulses and evolve by processes such as diffusion and mixing. We show that, in such environments, physical limits on the accuracy of temporal gradient sensing govern when and where bacteria can accurately measure the cues they use to navigate. Chemical pulses are surrounded by a predictable dynamic region, outside which bacterial cells cannot resolve gradients above noise. The outer boundary of this region initially expands in proportion to the square root of time before rapidly contracting. Our analysis also reveals how chemokinesis-the increase in swimming speed many bacteria exhibit when absolute chemical concentration exceeds a threshold-may serve to enhance chemotactic accuracy and sensitivity when the chemical landscape is dynamic. More generally, our framework provides a rigorous method for partitioning bacteria into populations that are 'near' and 'far' from chemical hotspots in complex, rapidly evolving environments such as those that dominate aquatic ecosystems.
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Affiliation(s)
- Andrew M Hein
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Douglas R Brumley
- Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Francesco Carrara
- Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Roman Stocker
- Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Simon A Levin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
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15
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Abstract
Chemotaxis underpins important ecological processes in marine bacteria, from the association with primary producers to the colonization of particles and hosts. Marine bacteria often swim with a single flagellum at high speeds, alternating "runs" with either 180° reversals or ∼90° "flicks," the latter resulting from a buckling instability of the flagellum. These adaptations diverge from Escherichia coli's classic run-and-tumble motility, yet how they relate to the strong and rapid chemotaxis characteristic of marine bacteria has remained unknown. We investigated the relationship between swimming speed, run-reverse-flick motility, and high-performance chemotaxis by tracking thousands of Vibrio alginolyticus cells in microfluidic gradients. At odds with current chemotaxis models, we found that chemotactic precision-the strength of accumulation of cells at the peak of a gradient-is swimming-speed dependent in V. alginolyticus Faster cells accumulate twofold more tightly by chemotaxis compared with slower cells, attaining an advantage in the exploitation of a resource additional to that of faster gradient climbing. Trajectory analysis and an agent-based mathematical model revealed that this unexpected advantage originates from a speed dependence of reorientation frequency and flicking, which were higher for faster cells, and was compounded by chemokinesis, an increase in speed with resource concentration. The absence of any one of these adaptations led to a 65-70% reduction in the population-level resource exposure. These findings indicate that, contrary to what occurs in E. coli, swimming speed can be a fundamental determinant of the gradient-seeking capabilities of marine bacteria, and suggest a new model of bacterial chemotaxis.
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16
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Live from under the lens: exploring microbial motility with dynamic imaging and microfluidics. Nat Rev Microbiol 2016; 13:761-75. [PMID: 26568072 DOI: 10.1038/nrmicro3567] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Motility is one of the most dynamic features of the microbial world. The ability to swim or crawl frequently governs how microorganisms interact with their physical and chemical environments, and underpins a myriad of microbial processes. The ability to resolve temporal dynamics through time-lapse video microscopy and the precise control of the physicochemical microenvironment afforded by microfluidics offer powerful new opportunities to study the many motility adaptations of microorganisms and thereby further our understanding of their ecology. In this Review, we outline recent insights into the motility strategies of microorganisms brought about by these techniques, including the hydrodynamic signature of microorganisms, their locomotion mechanics, chemotaxis, their motility near and on surfaces, swimming in moving fluids and motility in dense microbial suspensions.
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17
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Bondoc KGV, Heuschele J, Gillard J, Vyverman W, Pohnert G. Selective silicate-directed motility in diatoms. Nat Commun 2016; 7:10540. [PMID: 26842428 PMCID: PMC4742965 DOI: 10.1038/ncomms10540] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 12/23/2015] [Indexed: 11/09/2022] Open
Abstract
Diatoms are highly abundant unicellular algae that often dominate pelagic as well as benthic primary production in the oceans and inland waters. Being strictly dependent on silica to build their biomineralized cell walls, marine diatoms precipitate 240 × 10(12) mol Si per year, which makes them the major sink in the global Si cycle. Dissolved silicic acid (dSi) availability frequently limits diatom productivity and influences species composition of communities. We show that benthic diatoms selectively perceive and behaviourally react to gradients of dSi. Cell speed increases under dSi-limited conditions in a chemokinetic response and, if gradients of this resource are present, increased directionality of cell movement promotes chemotaxis. The ability to exploit local and short-lived dSi hotspots using a specific search behaviour likely contributes to micro-scale patch dynamics in biofilm communities. On a global scale this behaviour might affect sediment-water dSi fluxes and biogeochemical cycling.
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Affiliation(s)
- Karen Grace V Bondoc
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Department of Chemistry and Earth Sciences, Friedrich-Schiller-Universität Jena, Lessingstrasse 8, D-07743 Jena, Germany.,Max Planck Institute for Chemical Ecology, Max Planck Fellow, Hans-Knöll-Str. 8, D-07745 Jena, Germany
| | - Jan Heuschele
- Centre for Ocean Life, National Institute of Aquatic Resources, Technical University of Denmark, Charlottenlund Slot, Jægersborg Allé, DK-2920 Charlottenlund, Denmark.,Department of Biology, Aquatic Ecology Unit, Lund University, SE-22362 Lund, Sweden
| | - Jeroen Gillard
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Gent, Krijgslaan 281, S8, 9000 Gent, Belgium.,California State University, Department of Biology, 9001 Stockdale Hwy, Bakersfield, California 93311, USA
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Gent, Krijgslaan 281, S8, 9000 Gent, Belgium
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Department of Chemistry and Earth Sciences, Friedrich-Schiller-Universität Jena, Lessingstrasse 8, D-07743 Jena, Germany.,Max Planck Institute for Chemical Ecology, Max Planck Fellow, Hans-Knöll-Str. 8, D-07745 Jena, Germany
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18
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Feng CY, Wei JF, Li YJ, Yang YS, Wang YH, Lu L, Zheng GX. An on-chip pollutant toxicity determination based on marine microalgal swimming inhibition. Analyst 2016; 141:1761-71. [DOI: 10.1039/c5an02384j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Microfluidics using marine microalgal swimming behavior as a sensor signal were developed for a rapid and high-throughput determination of pollutant toxicity.
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Affiliation(s)
- Cheng-Yu Feng
- Chemical and Environmental Engineering Institute
- Dalian University
- Dalian
- China
- Microfluidic Research Institute
| | - Jun-Feng Wei
- Chemical and Environmental Engineering Institute
- Dalian University
- Dalian
- China
- Microfluidic Research Institute
| | - Ya-Jie Li
- Medical School
- Dalian University
- Dalian
- China
- Microfluidic Research Institute
| | - Yu-Suo Yang
- Chemical and Environmental Engineering Institute
- Dalian University
- Dalian
- China
- Microfluidic Research Institute
| | - Yun-Hua Wang
- Medical School
- Dalian University
- Dalian
- China
- Microfluidic Research Institute
| | - Ling Lu
- Medical School
- Dalian University
- Dalian
- China
- Microfluidic Research Institute
| | - Guo-Xia Zheng
- Chemical and Environmental Engineering Institute
- Dalian University
- Dalian
- China
- Microfluidic Research Institute
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19
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Watteaux R, Stocker R, Taylor JR. Sensitivity of the rate of nutrient uptake by chemotactic bacteria to physical and biological parameters in a turbulent environment. J Theor Biol 2015; 387:120-35. [DOI: 10.1016/j.jtbi.2015.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/09/2015] [Accepted: 08/01/2015] [Indexed: 12/22/2022]
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20
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Tout J, Jeffries TC, Petrou K, Tyson GW, Webster NS, Garren M, Stocker R, Ralph PJ, Seymour JR. Chemotaxis by natural populations of coral reef bacteria. ISME JOURNAL 2015; 9:1764-77. [PMID: 25615440 DOI: 10.1038/ismej.2014.261] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 12/01/2014] [Accepted: 12/05/2014] [Indexed: 12/27/2022]
Abstract
Corals experience intimate associations with distinct populations of marine microorganisms, but the microbial behaviours underpinning these relationships are poorly understood. There is evidence that chemotaxis is pivotal to the infection process of corals by pathogenic bacteria, but this evidence is limited to experiments using cultured isolates under laboratory conditions. We measured the chemotactic capabilities of natural populations of coral-associated bacteria towards chemicals released by corals and their symbionts, including amino acids, carbohydrates, ammonium and dimethylsulfoniopropionate (DMSP). Laboratory experiments, using a modified capillary assay, and in situ measurements, using a novel microfabricated in situ chemotaxis assay, were employed to quantify the chemotactic responses of natural microbial assemblages on the Great Barrier Reef. Both approaches showed that bacteria associated with the surface of the coral species Pocillopora damicornis and Acropora aspera exhibited significant levels of chemotaxis, particularly towards DMSP and amino acids, and that these levels of chemotaxis were significantly higher than that of bacteria inhabiting nearby, non-coral-associated waters. This pattern was supported by a significantly higher abundance of chemotaxis and motility genes in metagenomes within coral-associated water types. The phylogenetic composition of the coral-associated chemotactic microorganisms, determined using 16S rRNA amplicon pyrosequencing, differed from the community in the seawater surrounding the coral and comprised known coral associates, including potentially pathogenic Vibrio species. These findings indicate that motility and chemotaxis are prevalent phenotypes among coral-associated bacteria, and we propose that chemotaxis has an important role in the establishment and maintenance of specific coral-microbe associations, which may ultimately influence the health and stability of the coral holobiont.
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Affiliation(s)
- Jessica Tout
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Thomas C Jeffries
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Katherina Petrou
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Melissa Garren
- Department of Civil and Environmental Engineering, Ralph M. Parsons Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Roman Stocker
- Department of Civil and Environmental Engineering, Ralph M. Parsons Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter J Ralph
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Justin R Seymour
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia
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21
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Forest MG, Phuworawong P, Wang Q, Zhou R. Rheological signatures in limit cycle behaviour of dilute, active, polar liquid crystalline polymers in steady shear. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2014; 372:rsta.2013.0362. [PMID: 25332387 PMCID: PMC4223670 DOI: 10.1098/rsta.2013.0362] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We consider the dilute regime of active suspensions of liquid crystalline polymers (LCPs), addressing issues motivated by our kinetic model and simulations in Forest et al. (Forest et al. 2013 Soft Matter 9, 5207-5222 (doi:10.1039/c3sm27736d)). In particular, we report unsteady two-dimensional heterogeneous flow-orientation attractors for pusher nanorod swimmers at dilute concentrations where passive LCP equilibria are isotropic. These numerical limit cycles are analogous to longwave (homogeneous) tumbling and kayaking limit cycles and two-dimensional heterogeneous unsteady attractors of passive LCPs in weak imposed shear, yet these states arise exclusively at semi-dilute concentrations where stable equilibria are nematic. The results in Forest et al. mentioned above compel two studies in the dilute regime that complement recent work of Saintillan & Shelley (Saintillan & Shelley 2013 C. R. Physique 14, 497-517 (doi:10.1016/j.crhy.2013.04.001)): linearized stability analysis of the isotropic state for nanorod pushers and pullers; and an analytical-numerical study of weakly and strongly sheared active polar nanorod suspensions to capture how particle-scale activation affects shear rheology. We find that weakly sheared dilute puller versus pusher suspensions exhibit steady versus unsteady responses, shear thickening versus thinning and positive versus negative first normal stress differences. These results further establish how sheared dilute nanorod pusher suspensions exhibit many of the characteristic features of sheared semi-dilute passive nanorod suspensions.
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Affiliation(s)
- M Gregory Forest
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Panon Phuworawong
- Department of Mathematics and Statistics, Old Dominion University, Norfolk, VA 23529, USA
| | - Qi Wang
- Department of Mathematics, University of South Carolina, Columbia, SC 29208, USA
| | - Ruhai Zhou
- Department of Mathematics and Statistics, Old Dominion University, Norfolk, VA 23529, USA
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22
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Hol FJH, Dekker C. Zooming in to see the bigger picture: microfluidic and nanofabrication tools to study bacteria. Science 2014; 346:1251821. [PMID: 25342809 DOI: 10.1126/science.1251821] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The spatial structure of natural habitats strongly affects bacterial life, ranging from nanoscale structural features that individual cells exploit for surface attachment, to micro- and millimeter-scale chemical gradients that drive population-level processes. Nanofabrication and microfluidics are ideally suited to manipulate the environment at those scales and have emerged as powerful tools with which to study bacteria. Here, we review the new scientific insights gained by using a diverse set of nanofabrication and microfluidic techniques to study individual bacteria and multispecies communities. This toolbox is beginning to elucidate disparate bacterial phenomena-including aging, electron transport, and quorum sensing-and enables the dissection of environmental communities through single-cell genomics. A more intimate integration of microfluidics, nanofabrication, and microbiology will enable further exploration of bacterial life at the smallest scales.
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Affiliation(s)
- Felix J H Hol
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands.
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23
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Liu QX, Herman PMJ, Mooij WM, Huisman J, Scheffer M, Olff H, van de Koppel J. Pattern formation at multiple spatial scales drives the resilience of mussel bed ecosystems. Nat Commun 2014; 5:5234. [DOI: 10.1038/ncomms6234] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 09/11/2014] [Indexed: 11/09/2022] Open
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24
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Frankel NW, Pontius W, Dufour YS, Long J, Hernandez-Nunez L, Emonet T. Adaptability of non-genetic diversity in bacterial chemotaxis. eLife 2014; 3. [PMID: 25279698 PMCID: PMC4210811 DOI: 10.7554/elife.03526] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 09/28/2014] [Indexed: 11/29/2022] Open
Abstract
Bacterial chemotaxis systems are as diverse as the environments that bacteria inhabit, but how much environmental variation can cells tolerate with a single system? Diversification of a single chemotaxis system could serve as an alternative, or even evolutionary stepping-stone, to switching between multiple systems. We hypothesized that mutations in gene regulation could lead to heritable control of chemotactic diversity. By simulating foraging and colonization of E. coli using a single-cell chemotaxis model, we found that different environments selected for different behaviors. The resulting trade-offs show that populations facing diverse environments would ideally diversify behaviors when time for navigation is limited. We show that advantageous diversity can arise from changes in the distribution of protein levels among individuals, which could occur through mutations in gene regulation. We propose experiments to test our prediction that chemotactic diversity in a clonal population could be a selectable trait that enables adaptation to environmental variability. DOI:http://dx.doi.org/10.7554/eLife.03526.001 Bacterial colonies are generally made up of genetically identical cells. Despite this, a closer look at the members of a bacterial colony shows that these cells can have very different behaviors. For example, some cells may grow more quickly than others, or be more resistant to antibiotics. The mechanisms driving this diversity are only beginning to be identified and understood. Escherichia coli bacteria can move towards, or away from, certain chemicals in their surrounding environment to help them navigate toward favorable conditions. This behavior is known as chemotaxis. The signals from all of these chemicals are processed in E. coli by just one set of proteins, which control the different behaviors that are needed for the bacteria to follow them. Different numbers of these proteins are found in different—but genetically identical—bacteria, and the number of proteins is linked to how the bacteria perform these behaviors. It has been suggested that diversity can be beneficial to the overall bacterial population, as it helps the population survive environmental changes. This suggests that the level of diversity in the population should adapt to the level of diversity in the environment. However, it remains unknown how this adaptation occurs. Frankel et al. developed and combined several models and simulations to investigate whether differences in chemotaxis protein production help an E. coli colony to survive. The models show that in different environments, it can be beneficial for the population as a whole if different cells have different responses to the chemicals present. For example, if a lot of a useful chemical is present, bacteria are more likely to survive by heading straight to the source. If not much chemical is detected, the bacteria may need to move in a more exploratory manner. Frankel et al. find that different amounts of chemotaxis proteins produce these different behaviors. To survive in a changing environment, it is therefore best for the E. coli colony to contain cells that have different amounts of these proteins. Frankel et al. propose that the variability of chemotaxis protein levels between genetically identical cells can change through mutations in the genes that control how many of the proteins are produced, and predict that such mutations allow populations to adapt to environmental changes. The environments simulated in the model were much simpler than would be found in the real world, and Frankel et al. describe experiments that are now being performed to confirm and expand on their results. The model could be used in the future to shed light on the behavior of other cells that are genetically identical but exhibit diverse behaviors, from other bacterial species to more complex cancer cells. DOI:http://dx.doi.org/10.7554/eLife.03526.002
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Affiliation(s)
- Nicholas W Frankel
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - William Pontius
- Department of Physics, Yale University, New Haven, United States
| | - Yann S Dufour
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Junjiajia Long
- Department of Physics, Yale University, New Haven, United States
| | | | - Thierry Emonet
- Department of Physics, Yale University, New Haven, United States
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25
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Abstract
Microfluidics has significantly contributed to the expansion of the frontiers of microbial ecology over the past decade by allowing researchers to observe the behaviors of microbes in highly controlled microenvironments, across scales from a single cell to mixed communities. Spatially and temporally varying distributions of organisms and chemical cues that mimic natural microbial habitats can now be established by exploiting physics at the micrometer scale and by incorporating structures with specific geometries and materials. In this article, we review applications of microfluidics that have resulted in insightful discoveries on fundamental aspects of microbial life, ranging from growth and sensing to cell-cell interactions and population dynamics. We anticipate that this flexible multidisciplinary technology will continue to facilitate discoveries regarding the ecology of microorganisms and help uncover strategies to control microbial processes such as biofilm formation and antibiotic resistance.
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Affiliation(s)
- Roberto Rusconi
- Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; , ,
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26
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Zheng GX, Li YJ, Qi LL, Liu XM, Wang H, Yu SP, Wang YH. Marine phytoplankton motility sensor integrated into a microfluidic chip for high-throughput pollutant toxicity assessment. MARINE POLLUTION BULLETIN 2014; 84:147-154. [PMID: 24882443 DOI: 10.1016/j.marpolbul.2014.05.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 05/07/2014] [Accepted: 05/08/2014] [Indexed: 06/03/2023]
Abstract
A microfluidic chip was designed to assess the toxicity of pollutants in a high-throughput way by using marine phytoplankton motility as a sensor signal. In this chip, multiple gradient generators (CGGs) with diffusible chambers enable large scale of dose-response bioassays to be performed in a simple way. Two mobile marine phytoplankton cells were confined on-chip and stimulated by 8 concentrations (generated by CGG) of Hg, Pb, Cu and phenol singly, as well as Cu and phenol jointly. CASA system was used to characterize motility by motile percentage (%MOT), curvilinear velocity (VCL), average path velocity (VAP) and straight line velocity (VSL). In all cases, dose-dependent inhibitions of motility were observed. In the present system, only 2h was needed to predict EC50. Thus, the developed microfluidic chip device was proved to be useful as a rapid/simple and high-throughput test method in marine pollution toxicity assessment.
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Affiliation(s)
- Guo-xia Zheng
- Chemical and Environmental Engineering Institute, Dalian University, Dalian, China; Microfluidic Research Institute, Dalian University, Dalian, China.
| | - Ya-jie Li
- Medical School, Dalian University, Dalian, China; Microfluidic Research Institute, Dalian University, Dalian, China
| | - Lin-lin Qi
- Chemical and Environmental Engineering Institute, Dalian University, Dalian, China; Medical School, Dalian University, Dalian, China
| | - Xian-ming Liu
- Microfluidic Research Institute, Dalian University, Dalian, China; Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Hu Wang
- Chemical and Environmental Engineering Institute, Dalian University, Dalian, China; Microfluidic Research Institute, Dalian University, Dalian, China
| | - Shu-ping Yu
- Chemical and Environmental Engineering Institute, Dalian University, Dalian, China; Microfluidic Research Institute, Dalian University, Dalian, China
| | - Yun-hua Wang
- Medical School, Dalian University, Dalian, China; Microfluidic Research Institute, Dalian University, Dalian, China.
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27
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van Vliet S, Hol FJH, Weenink T, Galajda P, Keymer JE. The effects of chemical interactions and culture history on the colonization of structured habitats by competing bacterial populations. BMC Microbiol 2014; 14:116. [PMID: 24884963 PMCID: PMC4032360 DOI: 10.1186/1471-2180-14-116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 05/01/2014] [Indexed: 02/01/2023] Open
Abstract
Background Bacterial habitats, such as soil and the gut, are structured at the micrometer scale. Important aspects of microbial life in such spatial ecosystems are migration and colonization. Here we explore the colonization of a structured ecosystem by two neutrally labeled strains of Escherichia coli. Using time-lapse microscopy we studied the colonization of one-dimensional arrays of habitat patches linked by connectors, which were invaded by the two E. coli strains from opposite sides. Results The two strains colonize a habitat from opposite sides by a series of traveling waves followed by an expansion front. When population waves collide, they branch into a continuing traveling wave, a reflected wave and a stationary population. When the two strains invade the landscape from opposite sides, they remain segregated in space and often one population will displace the other from most of the habitat. However, when the strains are co-cultured before entering the habitats, they colonize the habitat together and do not separate spatially. Using physically separated, but diffusionally coupled, habitats we show that colonization waves and expansion fronts interact trough diffusible molecules, and not by direct competition for space. Furthermore, we found that colonization outcome is influenced by a culture’s history, as the culture with the longest doubling time in bulk conditions tends to take over the largest fraction of the habitat. Finally, we observed that population distributions in parallel habitats located on the same device and inoculated with cells from the same overnight culture are significantly more similar to each other than to patterns in identical habitats located on different devices inoculated with cells from different overnight cultures, even tough all cultures were started from the same −80°C frozen stock. Conclusions We found that the colonization of spatially structure habitats by two interacting populations can lead to the formation of complex, but reproducible, spatiotemporal patterns. Furthermore, we showed that chemical interactions between two populations cause them to remain spatially segregated while they compete for habitat space. Finally, we observed that growth properties in bulk conditions correlate with the outcome of habitat colonization. Together, our data show the crucial roles of chemical interactions between populations and a culture’s history in determining the outcome of habitat colonization.
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Affiliation(s)
- Simon van Vliet
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, Delft, CJ 2628, The Netherlands.
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28
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Schuech R, Menden-Deuer S. Going ballistic in the plankton: Anisotropic swimming behavior of marine protists. ACTA ACUST UNITED AC 2014. [DOI: 10.1215/21573689-2647998] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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29
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De Lillo F, Cencini M, Durham WM, Barry M, Stocker R, Climent E, Boffetta G. Turbulent fluid acceleration generates clusters of gyrotactic microorganisms. PHYSICAL REVIEW LETTERS 2014; 112:044502. [PMID: 24580457 DOI: 10.1103/physrevlett.112.044502] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Indexed: 06/03/2023]
Abstract
The motility of microorganisms is often biased by gradients in physical and chemical properties of their environment, with myriad implications on their ecology. Here we show that fluid acceleration reorients gyrotactic plankton, triggering small-scale clustering. We experimentally demonstrate this phenomenon by studying the distribution of the phytoplankton Chlamydomonas augustae within a rotating tank and find it to be in good agreement with a new, generalized model of gyrotaxis. When this model is implemented in a direct numerical simulation of turbulent flow, we find that fluid acceleration generates multifractal plankton clustering, with faster and more stable cells producing stronger clustering. By producing accumulations in high-vorticity regions, this process is fundamentally different from clustering by gravitational acceleration, expanding the range of mechanisms by which turbulent flows can impact the spatial distribution of active suspensions.
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Affiliation(s)
- Filippo De Lillo
- Dipartimento di Fisica and INFN, Università di Torino, via P. Giuria 1, 10125 Torino, Italy
| | - Massimo Cencini
- Istituto dei Sistemi Complessi, Consiglio Nazionale delle Ricerche, via dei Taurini 19, 00185 Rome, Italy
| | - William M Durham
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
| | - Michael Barry
- Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Roman Stocker
- Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Eric Climent
- Institut de Mécanique des Fluides, Université de Toulouse, INPT-UPS-CNRS, Allée du Pr. Camille Soula, F-31400 Toulouse, France
| | - Guido Boffetta
- Dipartimento di Fisica and INFN, Università di Torino, via P. Giuria 1, 10125 Torino, Italy
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Proteomic and transcriptomic analyses of "Candidatus Pelagibacter ubique" describe the first PII-independent response to nitrogen limitation in a free-living Alphaproteobacterium. mBio 2013; 4:e00133-12. [PMID: 24281717 PMCID: PMC3870248 DOI: 10.1128/mbio.00133-12] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Nitrogen is one of the major nutrients limiting microbial productivity in the ocean, and as a result, most marine microorganisms have evolved systems for responding to nitrogen stress. The highly abundant alphaproteobacterium "Candidatus Pelagibacter ubique," a cultured member of the order Pelagibacterales (SAR11), lacks the canonical GlnB, GlnD, GlnK, and NtrB/NtrC genes for regulating nitrogen assimilation, raising questions about how these organisms respond to nitrogen limitation. A survey of 266 Alphaproteobacteria genomes found these five regulatory genes nearly universally conserved, absent only in intracellular parasites and members of the order Pelagibacterales, including "Ca. Pelagibacter ubique." Global differences in mRNA and protein expression between nitrogen-limited and nitrogen-replete cultures were measured to identify nitrogen stress responses in "Ca. Pelagibacter ubique" strain HTCC1062. Transporters for ammonium (AmtB), taurine (TauA), amino acids (YhdW), and opines (OccT) were all elevated in nitrogen-limited cells, indicating that they devote increased resources to the assimilation of nitrogenous organic compounds. Enzymes for assimilating amine into glutamine (GlnA), glutamate (GltBD), and glycine (AspC) were similarly upregulated. Differential regulation of the transcriptional regulator NtrX in the two-component signaling system NtrY/NtrX was also observed, implicating it in control of the nitrogen starvation response. Comparisons of the transcriptome and proteome supported previous observations of uncoupling between transcription and translation in nutrient-deprived "Ca. Pelagibacter ubique" cells. Overall, these data reveal a streamlined, PII-independent response to nitrogen stress in "Ca. Pelagibacter ubique," and likely other Pelagibacterales, and show that they respond to nitrogen stress by allocating more resources to the assimilation of nitrogen-rich organic compounds. IMPORTANCE Pelagibacterales are extraordinarily abundant and play a pivotal role in marine geochemical cycles, as one of the major recyclers of labile dissolved organic matter. They are also models for understanding how streamlining selection can reshape chemoheterotroph metabolism. Streamlining and its broad importance to environmental microbiology are emerging slowly from studies that reveal the complete genomes of uncultured organisms. Here, we report another remarkable example of streamlined metabolism in Pelagibacterales, this time in systems that control nitrogen assimilation. Pelagibacterales are major contributors to metatranscriptomes and metaproteomes from ocean systems, where patterns of gene expression are used to gain insight into ocean conditions and geochemical cycles. The data presented here supply background that is essential to interpreting data from field studies.
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Abstract
Intuitively, it may seem that from the perspective of an individual bacterium the ocean is a vast, dilute, and largely homogeneous environment. Microbial oceanographers have typically considered the ocean from this point of view. In reality, marine bacteria inhabit a chemical seascape that is highly heterogeneous down to the microscale, owing to ubiquitous nutrient patches, plumes, and gradients. Exudation and excretion of dissolved matter by larger organisms, lysis events, particles, animal surfaces, and fluxes from the sediment-water interface all contribute to create strong and pervasive heterogeneity, where chemotaxis may provide a significant fitness advantage to bacteria. The dynamic nature of the ocean imposes strong selective pressures on bacterial foraging strategies, and many marine bacteria indeed display adaptations that characterize their chemotactic motility as "high performance" compared to that of enteric model organisms. Fast swimming speeds, strongly directional responses, and effective turning and steering strategies ensure that marine bacteria can successfully use chemotaxis to very rapidly respond to chemical gradients in the ocean. These fast responses are advantageous in a broad range of ecological processes, including attaching to particles, exploiting particle plumes, retaining position close to phytoplankton cells, colonizing host animals, and hovering at a preferred height above the sediment-water interface. At larger scales, these responses can impact ocean biogeochemistry by increasing the rates of chemical transformation, influencing the flux of sinking material, and potentially altering the balance of biomass incorporation versus respiration. This review highlights the physical and ecological processes underpinning bacterial motility and chemotaxis in the ocean, describes the current state of knowledge of chemotaxis in marine bacteria, and summarizes our understanding of how these microscale dynamics scale up to affect ecosystem-scale processes in the sea.
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Park D, Park SJ, Cho S, Lee Y, Lee YK, Min JJ, Park BJ, Ko SY, Park JO, Park S. Motility analysis of bacteria-based microrobot (bacteriobot) using chemical gradient microchamber. Biotechnol Bioeng 2013; 111:134-43. [DOI: 10.1002/bit.25007] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 07/08/2013] [Accepted: 07/15/2013] [Indexed: 01/04/2023]
Affiliation(s)
- Daechul Park
- School of Mechanical Systems Engineering; Chonnam National University; Gwangju 500-757 Korea
| | - Sung Jun Park
- School of Mechanical Systems Engineering; Chonnam National University; Gwangju 500-757 Korea
| | - Sunghoon Cho
- School of Mechanical Systems Engineering; Chonnam National University; Gwangju 500-757 Korea
| | - Yeonkyung Lee
- School of Mechanical Systems Engineering; Chonnam National University; Gwangju 500-757 Korea
| | - Yu Kyung Lee
- School of Mechanical Systems Engineering; Chonnam National University; Gwangju 500-757 Korea
| | - Jung-Joon Min
- Department of Nuclear Medicine; Chonnam National University Medical School; Gwangju Korea
| | - Bang Ju Park
- College of BioNano Technology; Gachon University; Gyeonggi-do Korea
| | - Seong Young Ko
- School of Mechanical Systems Engineering; Chonnam National University; Gwangju 500-757 Korea
| | - Jong-Oh Park
- School of Mechanical Systems Engineering; Chonnam National University; Gwangju 500-757 Korea
| | - Sukho Park
- School of Mechanical Systems Engineering; Chonnam National University; Gwangju 500-757 Korea
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Phytoplankton growth and microzooplankton grazing in the subtropical Northeast Atlantic. PLoS One 2013; 8:e69159. [PMID: 23935946 PMCID: PMC3720584 DOI: 10.1371/journal.pone.0069159] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 06/11/2013] [Indexed: 11/19/2022] Open
Abstract
Dilution experiments were performed to estimate phytoplankton growth and microzooplankton grazing rates during two Lagrangian surveys in inner and eastern locations of the Eastern North Atlantic Subtropical Gyre province (NAST-E). Our design included two phytoplankton size fractions (0.2–5 µm and >5 µm) and five depths, allowing us to characterize differences in growth and grazing rates between size fractions and depths, as well as to estimate vertically integrated measurements. Phytoplankton growth rates were high (0.11–1.60 d−1), especially in the case of the large fraction. Grazing rates were also high (0.15–1.29 d−1), suggesting high turnover rates within the phytoplankton community. The integrated balances between phytoplankton growth and grazing losses were close to zero, although deviations were detected at several depths. Also, O2 supersaturation was observed up to 110 m depth during both Lagrangian surveys. These results add up to increased evidence indicating an autotrophic metabolic balance in oceanic subtropical gyres.
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Wu J, Wu X, Lin F. Recent developments in microfluidics-based chemotaxis studies. LAB ON A CHIP 2013; 13:2484-99. [PMID: 23712326 DOI: 10.1039/c3lc50415h] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Microfluidic devices can better control cellular microenvironments compared to conventional cell migration assays. Over the past few years, microfluidics-based chemotaxis studies showed a rapid growth. New strategies were developed to explore cell migration in manipulated chemical gradients. In addition to expanding the use of microfluidic devices for a broader range of cell types, microfluidic devices were used to study cell migration and chemotaxis in complex environments. Furthermore, high-throughput microfluidic chemotaxis devices and integrated microfluidic chemotaxis systems were developed for medical and commercial applications. In this article, we review recent developments in microfluidics-based chemotaxis studies and discuss the new trends in this field observed over the past few years.
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Affiliation(s)
- Jiandong Wu
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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35
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Graff JR, Forschner-Dancause SR, Menden-Deuer S, Long RA, Rowley DC. Vibrio cholerae Exploits Sub-Lethal Concentrations of a Competitor-Produced Antibiotic to Avoid Toxic Interactions. Front Microbiol 2013; 4:8. [PMID: 23386845 PMCID: PMC3559943 DOI: 10.3389/fmicb.2013.00008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 01/08/2013] [Indexed: 11/29/2022] Open
Abstract
Vibrio cholerae is a human pathogenic marine bacterium inhabiting coastal regions and is vectored into human food and water supplies via attachment to particles including detritus, phytoplankton, and zooplankton. Particle colonization by the pathogen is inhibited by an antagonistic interaction with the particle-associated Vibrionales bacterium SWAT3, a producer of the antibiotic andrimid. By analyzing the individual movement behaviors of V. cholerae exposed to a gradient of andrimid in a microfluidics device, we show that the pathogen has a concentration dependent avoidance response to sub-lethal concentrations of the pure antibiotic and to the metabolites produced by a growing colony of SWAT3-wild-type. This avoidance behavior includes a 25% increase in swimming speeds, 30% increase in run lengths, and a shift in the direction of the bacteria away from the andrimid source. Consequently, these behavioral shifts at low concentrations of andrimid would lead to higher diffusivity and result in the dispersion of bacteria away from the competitor and source of the antibiotic. Such alterations in motility were not elicited in response to a non-andrimid-producing SWAT3 mutant, suggesting andrimid may be a negative effector of chemotaxis for V. cholerae. The behavioral response of colonizing bacteria to sub-inhibitory concentrations of competitor-produced antibiotics is one mechanism that can influence microbial diversity and interspecific competition on particles, potentially affecting human health in coastal communities and element cycling in the ocean.
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Affiliation(s)
- Jason R. Graff
- Graduate School of Oceanography, University of Rhode IslandNarragansett, RI, USA
| | | | - Susanne Menden-Deuer
- Graduate School of Oceanography, University of Rhode IslandNarragansett, RI, USA
| | - Richard A. Long
- Department of Biological Sciences and Marine Science Program, University of South CarolinaColumbia, SC, USA
| | - David C. Rowley
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode IslandKingston, RI, USA
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Abstract
Bacteria play an indispensable role in marine biogeochemistry by recycling dissolved organic matter. Motile species can exploit small, ephemeral solute patches through chemotaxis and thereby gain a fitness advantage over nonmotile competitors. This competition occurs in a turbulent environment, yet turbulence is generally considered inconsequential for bacterial uptake. In contrast, we show that turbulence affects uptake by stirring nutrient patches into networks of thin filaments that motile bacteria can readily exploit. We find that chemotactic motility is subject to a trade-off between the uptake benefit due to chemotaxis and the cost of locomotion, resulting in an optimal swimming speed. A second trade-off results from the competing effects of stirring and mixing and leads to the prediction that chemotaxis is optimally favored at intermediate turbulence intensities.
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Affiliation(s)
- John R Taylor
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK
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37
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Durham WM, Stocker R. Thin phytoplankton layers: characteristics, mechanisms, and consequences. ANNUAL REVIEW OF MARINE SCIENCE 2012; 4:177-207. [PMID: 22457973 DOI: 10.1146/annurev-marine-120710-100957] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
For over four decades, aggregations of phytoplankton known as thin layers have been observed to harbor large amounts of photosynthetic cells within narrow horizontal bands. Field observations have revealed complex linkages among thin phytoplankton layers, the physical environment, cell behavior, and higher trophic levels. Several mechanisms have been proposed to explain layer formation and persistence, in the face of the homogenizing effect of turbulent dispersion. The challenge ahead is to connect mechanistic hypotheses with field observations to gain better insight on the phenomena that shape layer dynamics. Only through a mechanistic understanding of the relevant biological and physical processes can we begin to predict the effect of thin layers on the ecology of phytoplankton and higher organisms.
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Affiliation(s)
- William M Durham
- Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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38
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Raposo EP, Bartumeus F, da Luz MGE, Ribeiro-Neto PJ, Souza TA, Viswanathan GM. How landscape heterogeneity frames optimal diffusivity in searching processes. PLoS Comput Biol 2011; 7:e1002233. [PMID: 22072951 PMCID: PMC3207935 DOI: 10.1371/journal.pcbi.1002233] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 09/02/2011] [Indexed: 01/19/2023] Open
Abstract
Theoretical and empirical investigations of search strategies typically have failed to distinguish the distinct roles played by density versus patchiness of resources. It is well known that motility and diffusivity of organisms often increase in environments with low density of resources, but thus far there has been little progress in understanding the specific role of landscape heterogeneity and disorder on random, non-oriented motility. Here we address the general question of how the landscape heterogeneity affects the efficiency of encounter interactions under global constant density of scarce resources. We unveil the key mechanism coupling the landscape structure with optimal search diffusivity. In particular, our main result leads to an empirically testable prediction: enhanced diffusivity (including superdiffusive searches), with shift in the diffusion exponent, favors the success of target encounters in heterogeneous landscapes.
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Affiliation(s)
- E P Raposo
- Laboratório de Física Teórica e Computacional, Departamento de Física, Universidade Federal de Pernambuco, Recife, Brazil.
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39
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Signalling and the evolution of cooperative foraging in dynamic environments. PLoS Comput Biol 2011; 7:e1002194. [PMID: 21966265 PMCID: PMC3178622 DOI: 10.1371/journal.pcbi.1002194] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 07/29/2011] [Indexed: 11/19/2022] Open
Abstract
Understanding cooperation in animal social groups remains a significant challenge for evolutionary theory. Observed behaviours that benefit others but incur some cost appear incompatible with classical notions of natural selection; however, these behaviours may be explained by concepts such as inclusive fitness, reciprocity, intra-specific mutualism or manipulation. In this work, we examine a seemingly altruistic behaviour, the active recruitment of conspecifics to a food resource through signalling. Here collective, cooperative behaviour may provide highly nonlinear benefits to individuals, since group functionality has the potential to be far greater than the sum of the component parts, for example by enabling the effective tracking of a dynamic resource. We show that due to this effect, signalling to others is an evolutionarily stable strategy under certain environmental conditions, even when there is a cost associated to this behaviour. While exploitation is possible, in the limiting case of a sparse, ephemeral but locally abundant nutrient source, a given environmental profile will support a fixed number of signalling individuals. Through a quantitative analysis, this effective carrying capacity for cooperation is related to the characteristic length and time scales of the resource field. One of the key challenges facing evolutionary theory is understanding how cooperation and communication evolve in social systems. In many situations cooperation leads to higher net benefits to all, but a population of cooperators is vulnerable to invasion from exploitative strategies. When foraging, aiding others through sharing information can lead to an advantage to a collective of communicating individuals. How this behaviour can be maintained and resist invasion without centralized control or policing is currently not clear. In this work, we examine a social foraging system where individuals evolve to signal to conspecifics when they locate a resource. We show that in some environments, cooperative signalling is sustained through a form of indirect reciprocation, as a signalling phenotype is more likely to be the beneficiary of a signal from a conspecific in the future. This effect naturally occurs as a result of the foraging dynamic and, depending on the environment, such as how resources are distributed and how difficult they are to track, will compensate for relatively large costs of signalling. Through simulations and a simplified model we examine the parameters driving this process and identify the mechanisms required for cooperation to evolve in such a system.
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40
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Abstract
Zooplankton is a morphologically and taxonomically diverse group and includes organisms that vary in size by many orders of magnitude, but they are all faced with the common problem of collecting food from a very dilute suspension. In order to maintain a viable population in the face of mortality, zooplankton in the ocean have to clear daily a volume of ambient water for prey particles that is equivalent to about 10(6) times their own body volume. While most size-specific vital rates and mortality rates decline with size, the clearance requirement is largely size-independent because food availability also declines with size. There is a limited number of solutions to the problem of concentrating dilute prey from a sticky medium: passive and active ambush feeding; feeding-current feeding, where the prey is either intercepted directly, retained on a filter, or individually perceived and extracted from the feeding current; cruise feeding; and colonization of large particles and marine snow aggregates. The basic mechanics of these food-collection mechanisms are described, and it is shown that their efficiencies are inherently different and that each of these mechanisms becomes less efficient with increasing size. Mechanisms that compensate for this decline in efficiency are described, including inflation of feeding structures and development of vision. Each feeding mode has implications beyond feeding in terms of risk of encountering predators and chance of meeting mates, and they partly target different types of prey. The main dichotomy is between (inefficient) ambush feeding on motile prey and the more efficient active feeding modes; a secondary dichotomy is between (efficient) hovering and (less efficient) cruising feeding modes. The efficiencies of the various feeding modes are traded off against feeding-mode-dependent metabolic expenses, predation risks, and mating chances. The optimality of feeding strategies, evaluated as the ratio of gain over risk, varies with the environment, and may explain both size-dependent and spatio-temporal differences in distributions of various feeding types as well as other aspects of the biology of zooplankton (mating behaviour, predator defence strategies).
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Affiliation(s)
- Thomas Kiørboe
- National Institute of Aquatic Resources, Technical University of Denmark, Kavalergården 6, Charlottenlund, Denmark.
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41
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Durham WM, Climent E, Stocker R. Gyrotaxis in a steady vortical flow. PHYSICAL REVIEW LETTERS 2011; 106:238102. [PMID: 21770545 DOI: 10.1103/physrevlett.106.238102] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Indexed: 05/11/2023]
Abstract
We show that gyrotactic motility within a steady vortical flow leads to tightly clustered aggregations of microorganisms. Two dimensionless numbers, characterizing the relative swimming speed and stability against overturning by vorticity, govern the coupling between motility and flow. Exploration of parameter space reveals a striking array of patchiness regimes. Aggregations are found to form within a few overturning time scales, suggesting that vortical flows might be capable of efficiently separating species with different motility characteristics.
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Affiliation(s)
- William M Durham
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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42
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Abstract
Locomotion is widely observed in life at micrometric scales and is exhibited by many eukaryotic unicellular organisms. Motility of such organisms can be achieved through periodic deformations of a tail-like projection called the eukaryotic flagellum. Although the mechanism allowing the flagellum to deform is largely understood, questions related to the functional significance of the observed beating patterns remain unresolved. Here, we focus our attention on the stroke patterns of biflagellated phytoplanktons resembling the green alga Chlamydomonas. Such organisms have been widely observed to beat their flagella in two different ways--a breaststroke and an undulatory stroke--both of which are prototypical of general beating patterns observed in eukaryotes. We develop a general optimization procedure to determine the existence of optimal swimming gaits and investigate their functional significance with respect to locomotion and nutrient uptake. Both the undulatory and the breaststroke represent local optima for efficient swimming. With respect to the generation of feeding currents, we found the breaststroke to be optimal and to enhance nutrient uptake significantly, particularly when the organism is immersed in a gradient of nutrients.
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43
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Menden-Deuer S. Inherent high correlation of individual motility enhances population dispersal in a heterotrophic, planktonic protist. PLoS Comput Biol 2010; 6:e1000942. [PMID: 20975936 PMCID: PMC2958803 DOI: 10.1371/journal.pcbi.1000942] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 08/25/2010] [Indexed: 11/29/2022] Open
Abstract
Quantitative linkages between individual organism movements and the resulting population distributions are fundamental to understanding a wide range of ecological processes, including rates of reproduction, consumption, and mortality, as well as the spread of diseases and invasions. Typically, quantitative data are collected on either movement behaviors or population distributions, rarely both. This study combines empirical observations and model simulations to gain a mechanistic understanding and predictive ability of the linkages between both individual movement behaviors and population distributions of a single-celled planktonic herbivore. In the laboratory, microscopic 3D movements and macroscopic population distributions were simultaneously quantified in a 1L tank, using automated video- and image-analysis routines. The vertical velocity component of cell movements was extracted from the empirical data and used to motivate a series of correlated random walk models that predicted population distributions. Validation of the model predictions with empirical data was essential to distinguish amongst a number of theoretically plausible model formulations. All model predictions captured the essence of the population redistribution (mean upward drift) but only models assuming long correlation times (minute), captured the variance in population distribution. Models assuming correlation times of 8 minutes predicted the least deviation from the empirical observations. Autocorrelation analysis of the empirical data failed to identify a de-correlation time in the up to 30-second-long swimming trajectories. These minute-scale estimates are considerably greater than previous estimates of second-scale correlation times. Considerable cell-to-cell variation and behavioral heterogeneity were critical to these results. Strongly correlated random walkers were predicted to have significantly greater dispersal distances and more rapid encounters with remote targets (e.g. resource patches, predators) than weakly correlated random walkers. The tendency to disperse rapidly in the absence of aggregative stimuli has important ramifications for the ecology and biogeography of planktonic organisms that perform this kind of random walk. Organism movement is fundamental to how organisms interact with each other and the environment. Such movements are also important on the population level and determine the spread of disease and invasion, reproduction, consumption, and mortality. Theoretical ecologists have sought to predict population dispersal rates, which are often hard to measure, from individual movement behaviors, which are often easier to measure. This problem has been non-trivial. This manuscript contributes seldom available, simultaneously measured movement behaviors and population distributions of a single celled planktonic organism. The empirical data are used to distinguish amongst a set of plausible theoretical modeling approaches to suggest that organism movements are highly correlated, meaning movement direction and speed is consistent over several minutes. Previous estimates suggested persistence only lasted several seconds. Minute-scale correlations result in much more rapid organism dispersal and greater dispersal distance, indicating that organisms encounter and impact a greater portion of their surrounding habitat than previously suspected.
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Affiliation(s)
- Susanne Menden-Deuer
- University of Rhode Island, Graduate School of Oceanography, Narragansett, Rhode Island, USA.
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44
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Ahmed T, Shimizu TS, Stocker R. Bacterial chemotaxis in linear and nonlinear steady microfluidic gradients. NANO LETTERS 2010; 10:3379-85. [PMID: 20669946 PMCID: PMC2935935 DOI: 10.1021/nl101204e] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Diffusion-based microfluidic devices can generate steady, arbitrarily shaped chemical gradients without requiring fluid flow and are ideal for studying chemotaxis of free-swimming cells such as bacteria. However, if microfluidic gradient generators are to be used to systematically study bacterial chemotaxis, it is critical to evaluate their performance with actual quantitative chemotaxis tests. We characterize and compare three diffusion-based gradient generators by confocal microscopy and numerical simulations, select an optimal design and apply it to chemotaxis experiments with Escherichia coli in both linear and nonlinear gradients. Comparison of the observed cell distribution along the gradients with predictions from an established mathematical model shows very good agreement, providing the first quantification of chemotaxis of free-swimming cells in steady nonlinear microfluidic gradients and opening the door to bacterial chemotaxis studies in gradients of arbitrary shape.
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Affiliation(s)
- Tanvir Ahmed
- Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA
| | - Thomas S. Shimizu
- FOM Institute for Atomic and Molecular Physics (AMOLF), Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Roman Stocker
- Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA
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Saintillan D. Extensional rheology of active suspensions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:056307. [PMID: 20866322 DOI: 10.1103/physreve.81.056307] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Indexed: 05/29/2023]
Abstract
A simple model is presented for the effective extensional rheology of a dilute suspension of active particles, such as self-propelled microswimmers, extending previous classical studies on suspensions of passive rodlike particles. Neglecting particle-particle hydrodynamic interactions, we characterize the configuration of the suspension by an orientation distribution, which satisfies a Fokker-Planck equation including the effects of an external flow field and of rotary diffusion. Knowledge of this orientation distribution then allows the determination of the particle extra stress as a configurational average of the force dipoles exerted by the particles on the fluid, which involve contributions from the imposed flow, rotary diffusion, and the permanent dipoles resulting from activity. Analytical expressions are obtained for the stress tensor in uniaxial extensional and compressional flows, as well as in planar extensional flow. In all types of flows, the effective viscosity is found to increase as a result of activity in suspensions of head-actuated swimmers (pullers) and to decrease in suspensions of tail-actuated swimmers (pushers). In the latter case, a negative particle viscosity is found to occur in weak flows. In planar extensional flow, we also characterize normal stresses, which are enhanced by activity in suspensions of pullers but reduced in suspensions of pushers. Finally, an energetic interpretation of the seemingly unphysical decrease in viscosity predicted in suspensions of pushers is proposed, where the decrease is explained as a consequence of the active power input generated by the swimming particles and is shown not to be directly related to viscous dissipative processes.
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Affiliation(s)
- David Saintillan
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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46
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Ahmed T, Shimizu TS, Stocker R. Microfluidics for bacterial chemotaxis. Integr Biol (Camb) 2010; 2:604-29. [DOI: 10.1039/c0ib00049c] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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47
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Biotech paper watch. Biotechnol J 2009. [DOI: 10.1002/biot.200990019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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