Scale-free vertical tracking microscopy

Krishnamurthy, Deepak; Li, Hongquan; Rey, François Benoit du; Cambournac, Pierre; Larson, Adam G.; Li, Ethan; Prakash, Manu

doi:10.1038/s41592-020-0924-7

Cited by 38 publications

(37 citation statements)

References 48 publications

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“…With simple modifications to the setup design, the lensless approach used here can be adopted for smaller organisms such as bacteria and heterotrophic nanoflagellates, or larger, such as rotifers, and small crustaceans. It could also be merged with rotating stages that keep cells in suspension [24] The method is particular suitable to study micro-zooplankton grazing behaviors.…”

Section: Discussionmentioning

confidence: 99%

Microplankton life histories revealed by holographic microscopy and deep learning

Bachimanchi¹,

Midtvedt²,

Midtvedt³

et al. 2022

Preprint

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The marine microbial food web plays a central role in the global carbon cycle. Our mechanistic understanding of the ocean, however, is biased towards its larger constituents, while rates and biomass fluxes in the microbial food web are mainly inferred from indirect measurements and ensemble averages. Yet, resolution at the level of the individual microplankton is required to advance our understanding of the oceanic food web. Here, we demonstrate that, by combining holographic microscopy with deep learning, we can follow microplanktons throughout their lifespan, continuously measuring their three dimensional position and dry mass. The deep learning algorithms circumvent the computationally intensive processing of holographic data and allow rapid measurements over extended time periods. This permits us to reliably estimate growth rates, both in terms of dry mass increase and cell divisions, as well as to measure trophic interactions between species such as predation events. The individual resolution provides information about selectivity, individual feeding rates and handling times for individual microplanktons. This method is particularly useful to explore the flux of carbon through micro-zooplankton, the most important and least known group of primary consumers in the global oceans. We exemplify this by detailed descriptions of microzooplankton feeding events, cell divisions, and long term monitoring of single cells from division to division.

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Section: Discussionmentioning

confidence: 99%

Microplankton life histories revealed by holographic microscopy and deep learning

Bachimanchi¹,

Midtvedt²,

Midtvedt³

et al. 2022

Preprint

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“…To study the multi-scale process of microscale near-field flows and macroscale sinking dynamics we leveraged Scale-free Vertical Tracking Microscopy (SVTM) [24] that uses controlled rotation of a circular "hydrodynamic treadmill" to automatically keep small objects centered in the microscope field-of-view while allowing free movement with no bounds along the axis of gravity (Fig. 2A).…”

Section: Experimental Systemmentioning

confidence: 99%

“…In this work, we present a novel experimental system and measurements combining agar aggregates colonized by Vorticella convallaria (our model "active sinking particles"), and Scale-free Vertical Tracking Microscopy, aka Gravity Machine [24]. This recent advance in tracking microscopy allows freely-sinking particles to be automatically tracked using a circular "hydrodynamic treadmill."…”

Section: Introductionmentioning

confidence: 99%

“…In this work, we present a novel experimental system and measurements combining agar aggregates colonized by Vorticella convallaria (our model “active sinking particles”), and Scale-free Vertical Tracking Microscopy, aka Gravity Machine [24]. This recent advance in tracking microscopy allows freely-sinking particles to be automatically tracked using a circular “hydrodynamic treadmill.” Using this novel method we present the first detailed measurements and characterizations of near-field flows around “active sinking particles” and find that they can be significantly modified by the presence of one or more Vorticella cells.…”

Section: Introductionmentioning

confidence: 99%

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Active Sinking Particles: Sessile Suspension Feeders significantly alter the Flow and Transport to Sinking Aggregates

Krishnamurthy

Pepper

Prakash

2021

Preprint

Self Cite

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Sinking or sedimentation of biological aggregates plays a critical role in carbon sequestration in the ocean and in vertical material fluxes in waste-water treatment plants. In both these contexts, the sinking aggregates are “active,” since they are hot-spots of biological life and are densely colonized by microorganisms including bacteria and sessile protists, some of which generate feeding currents. However, the effect of these feeding currents on the sinking rates, trajectories, and mass transfer to these “active sinking particles,” has not previously been studied. Here we use a novel scale-free vertical-tracking microscope (a.k.a. Gravity Machine, Krishnamurthy et al. “Scale-free vertical tracking microscopy.” Nature Methods (2020)) to follow model sinking aggregates (agar spheres) with attached protists (Vorticella convallaria), sinking over long distances while simultaneously measuring local flows. We find that activity generated by attached Vorticella cause substantial changes to the flow around aggregates in a dynamic manner and reshape mass transport boundary layers. Further, we find that activity-mediated local flows along with sinking significantly changes how aggregates interact with the water-column at larger scales by modifying the encounter and plume cross-sections and by inducing sustained aggregate rotations. In this way our work suggests an important role of biological activity in understanding the growth, degradation, composition and sinking speeds of aggregates with consequences for predicting vertical material fluxes in marine, freshwater and man-made environments.1Significance StatementSinking aggregates are a critical part of aquatic ecosystems. Plentiful sinking aggregates account for the majority of carbon sequestration in the oceans. These aggregates are densely colonized by microorganisms, including many that generate feeding currents. Utilizing a novel instrument for high resolution imaging of sinking particles, we demonstrate that these feeding currents significantly change how water flows near the aggregates. We show that these changes in flow are likely to affect aquatic system processes, including aggregation rates, degradation rates, sinking speeds, and aggregate composition. Our work provides a starting point for exploring the larger-scale implications of attached organisms on these system processes, which, in turn, are critical for understanding carbon sequestration in the oceans or efficiency in waste-water treatment plants.

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“…Another example is that after the food source (prey phytoplankton, Isochrysis galbana) was introduced, the turning rate of swimming tracks of predator phytoplankton Oxyrrhis marina-a wide distributed red tide organismsignificantly increased, and at the same time the vertical velocities of O. marina significantly decreased [5,17]. Further, a scale-free, vertical tracking microscope was developed for observing multiscale behavioral of single cells, e.g., nonadherent planktonic cells and organisms [18]. These modern techniques provide efficient tools for tracking the behavior of phytoplankton movements response to environmental change.…”

Section: Introductionmentioning

confidence: 99%

Fat Tail in the Phytoplankton Movement Patterns and Swimming Behavior: New Insights into the Prey-Predator Interactions

Xiao

et al. 2021

Fractal Fract

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Phytoplankton movement patterns and swimming behavior are important and basic topics in aquatic biology. Heavy tail distribution exists in diverse taxa and shows theoretical advantages in environments. The fat tails in the movement patterns and swimming behavior of phytoplankton in response to the food supply were studied. The log-normal distribution was used for fitting the probability density values of the movement data of Oxyrrhis marina. Results showed that obvious fat tails exist in the movement patterns of O. marina without and with positive stimulations of food supply. The algal cells tended to show a more chaotic and disorderly movement, with shorter and neat steps after adding the food source. At the same time, the randomness of turning rate, path curvature and swimming speed increased in O. marina cells with food supply. Generally, the responses of phytoplankton movement were stronger when supplied with direct prey cells rather than the cell-free filtrate. The scale-free random movements are considered to benefit the adaption of the entire phytoplankton population to varied environmental conditions. Inferentially, the movement pattern of O. marina should also have the characteristics of long-range dependence, local self-similarity and a system of fractional order.

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Scale-free vertical tracking microscopy

Cited by 38 publications

References 48 publications

Microplankton life histories revealed by holographic microscopy and deep learning

Microplankton life histories revealed by holographic microscopy and deep learning

Active Sinking Particles: Sessile Suspension Feeders significantly alter the Flow and Transport to Sinking Aggregates

Fat Tail in the Phytoplankton Movement Patterns and Swimming Behavior: New Insights into the Prey-Predator Interactions

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