Imaging-based solutions to observe ecological processes at different length scales
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Author
Date
2023Type
- Doctoral Thesis
ETH Bibliography
yes
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Abstract
Ecological processes comprise all physical phenomena and organism activities that shape ecosystems. They are ubiquitous in the environment at all length scales, sustain biodiversity and apply selective pressure, driving evolution. Their study provides us with an understanding of the functioning of ecosystems. Some of these ecological processes require specialized technologies for their study, particularly ones that are invisible to the naked eye or take place in difficult-to-access locations. In this thesis, we expand the ecologists’ toolbox by developing three image-based solutions to study three ecological processes at different length scales.
First, in Chapter 2, we developed the Microbial Landscape Device (MicroLanD), a microfluidic platform that can mimic the heterogeneous and ephemeral nature of the microbial nutrient landscape to study microbial foraging. Microbial foraging plays a vital role in the biogeochemical cycling of nutrients and forms a trophic pathway sustaining higher-order organisms. MicroLanD is able to automatically generate complex and dynamic nutrient landscapes via four hydrogel ports that deliver soluble substrates into an arena where bacterial foraging can be observed in real-time using video microscopy. The nutrient delivery characteristics of MicroLanD were characterized, and MicroLanD was tested in two foraging experiments in which the behavioural response of a population of marine bacteria to a complex spatiotemporal landscape of nutrients was characterized for up to 12 h.
The experience gained through the development of MicroLanD was applied to characterize a fascinating predation strategy in Chapter 3. In this predation strategy, called backpack formation, the amoeba Acanthamoeba castellanii traps the bacteria Listeria monocytogenes in aggregates or backpacks on its posterior prior to consumption via phagocytosis. The mechanism driving this predator-prey interaction had previously remained unknown. Through the combination of video microscopy observations from experiments in microfluidic devices with single-cell tracking algorithms, we determined that random encounters, enhanced by Listeria motility and Acanthamoeba locomotion, are responsible for backpack formation. The microfluidic approach and single-cell tracking algorithms described in this chapter further provide a blueprint for studies that aim to disentangle microscale dynamics between microorganisms.
For the third image-based solution, in Chapter 4, we shifted the focus from a laboratory setting to a natural stream in the environment. Small riverine organisms, such as benthic invertebrates and juvenile fish, use river flow as an essential physical pathway to disperse downstream and occupy other habitats. This process is called drift and is a crucial element in the life cycle of many taxa. Riverine organism drift is traditionally studied using logistically demanding and labour-intensive net-based methods. The Riverine Organism Drift Imager (RODI) we developed and deployed expands on the traditional methodology by replacing the collection cup with a flow-through, non-invasive camera system, combined with modern image-processing and machine-learning techniques, allowing for the study of small riverine organism drift with unparalleled resolution. Through multiple deployments in a Swiss alpine river, we demonstrated that RODI can produce images of sufficient quality for organisms to be identified to at least the family level. This novel approach drastically streamlines the sampling of small riverine organisms and could be applied broadly as a tool for biodiversity monitoring and scientific studies, contributing to the development of efficient river management strategies for the conservation of aquatic biota. Show more
Permanent link
https://doi.org/10.3929/ethz-b-000649707Publication status
publishedExternal links
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Contributors
Examiner: Stocker, Roman
Examiner: Ackermann, Martin
Examiner: Jaffe, Jules S.
Examiner: Robinson, Christopher
Examiner: Silva, Luiz G.M.
Examiner: Raitoharju, Jenni
Publisher
ETH ZurichSubject
Ecology; Computer Vision; Microbial ecology; Aquatic ecology; Technology developmentOrganisational unit
09467 - Stocker, Roman / Stocker, Roman
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