NanoBio – microworkshop: Biology on a chip

Biology on a chip 

Associate Professor Edith Hammer at Dept Biology

Edith is a soil biologist working with various types of microfluidic devices for fundamental studies of soil and soil based microorganisms with strong relevance for ecology, climate and environment.

https://portal.research.lu.se/en/persons/edith-hammer

Microbial interactions with the soil ecosystem at the micrometer scale in microfluidic soil chips

Edith Hammer, Kristin Aleklett, Micaela Mafla Endara, Milda Pucetaite, Pelle Ohlsson, Fredrik Klinghammer, Hanbang Zou, Carlos Arellano

Microbial experiments can classically be performed either highly controlled in the laboratory, or under realistic conditions in the field, with trade-offs to both approaches. We are developing microfluidic soil chips that help to bridge the two extremes: they constitute transparent proxies of the soil pore space that microorganisms voluntarily colonize, enabling us to conduct controlled studies with soil microbial communities at cellular scale, either by incubating the soil chips in the field or using cultures and soil inocula in the lab. We studied fungal hyphal reactions to different spatial structures including fractal mazes. We can monitor fungal resource allocation to different spatial structures by measuring their cytoplasm allocation and retraction. We have studied the impact of fungal hyphae on the dispersal capability of both bacteria and protists moving out of soil (“fungal highways”), showing that hyphal presence increased the distance the organisms can reach, and their population sizes several fold. By monitoring soil communities in the chips, we have been able to report unusual trophic interactions like fungal nematode and protist predation, as well as fungivorous bacteria and protists, supplementing our understanding of soil trophic food webs. Studying label-free microorganisms from soil samples requires advanced image analysis that we currently are developing with deep learning approaches. The image derived morphodata can be a valuable complement to molecular community analysis. Last but not least, the soil chips enable us to peek into the opaque soil environement, enabling us to better communicate the vulnerable but beautiful soil ecosystem to society.

For more information, see the associated youtube channel and a few scientific publications:

https://www.youtube.com/@Soilwatching

https://www.nature.com/articles/s42003-021-02379-5

https://www.cell.com/current-biology/pdfExtended/S0960-9822(23)00237-3

https://www.nature.com/articles/ismej2017184