Course: Assessment of microbial communities and their functions using microsensors and visualization techniques

Time: 15.-19.11.2021
Mode of delivery: Hybrid course (online lecture, on campus laboratory work)
Extent: 1 to 3 ECTS
Language: English
Close-up picture of pipetting in bio-medicine laboratory


Microbes catalyze many processes that affect our lives both positively and negatively. Microbially catalyzed processes are utilized in many industrial applications, agriculture, water treatment and food production. Microbial activity depends largely on local environmental conditions and the composition and spatial structure of the microbial community. One important regulator of microbial activity is oxygen availability in the system and oxygen gradients can be quite pronounced. Microsensors are used to measure gradients of oxygen and other gases such as nitrous oxide, hydrogen sulfide and hydrogen in very high spatial resolution, e.g., in plant and animal tissues, biofilms and soils. This very precise measurement of environmental parameters can be combined with visualization techniques to identify hotspots of microbial activity in a system and quantitative PCR to determine the abundance of certain taxonomic groups or functional genes. Special staining techniques can be used e.g., to differentiate between living and dead cells, to identify active cells and to label individual taxonomic groups using a fluorescence in situ hybridization (FISH) techniques. The stained cells can then be analyzed microscopically to observe their distribution or quantified using fluorescence readers.

This course will give participants hands-on experience on using microsensors in different setups, labelling microbial cells and subsequent microscopic and quantitative analysis to determine the distribution and abundance of microbial groups involved in the process of interest..

Aims of the course

In this course, students will learn how to use different types of microsensors in a variety of experimental setups and how to interpret the obtained results. Microsensor measurements will be complemented by characterization of the microbial communities through visualization techniques. The course will provide a platform for interaction between students, researchers and experts in the field, which will allow for sharing of ideas and experiences.

Target group

The course is planned as postgraduate course but will be suitable also for master students from technical and natural sciences with pronounced interest in the topic. The course is organized as an intensive short course (1 week) including online lectures, laboratory exercises (on campus) and other learning activities. The course is aimed at students and researchers in the following fields:

  • Microbiology
  • Microbial ecology
  • Ecology
  • Environmental engineering
  • Water treatment
  • Analytical technologies and methodologies


Course lecturers include:

  • Prof. Akihiko Terada, Tokyo University of Agriculture and Technology, Japan
  • Prof. Jessica Mark Welch, University of Chicago, USA
  • Unisense expert, Unisense, Denmark
  • Doc. Katharina Kujala, University of Oulu, Finland

Registrations and contact information

Registration by November 7th, 2021 in this link

For questions concerning the course please contact Katharina Kujala (Katharina.kujala at


* The times might change, the registered participants will be informed about the changes.

Monday November 15

09:30-10:00 Introduction to the course (Katharina Kujala)

10:00-11:30 Principles of microsensor measurements (Unisense)

11:30-12:30 Lunch break

12:30- 16:00 Laboratory experiments

Tuesday November 16

09:30-11:00 Lecture on microscopy techniques (Janne Koskimäki)

11:00-12:30 Lunch break

12:00-16:00 Laboratory experiments

16:00-17:00 Lecture on visualization techniques to investigate the spatial organization of microbial communities (Jessica Mark Welch)

Wednesday November 17

09:00-10:0 Lecture on the use of inhibitors in incubation experiments (Katharina Kujala)


14:00-16:00 Demonstration of microscopy equipment at the Biocenter microscopy facilities (medical campus)

Thursday November 18

09:00-11:30 Online group session to discuss microsensor applications and staining techniques

11:30-12:30 Lunch break

12:30- 16:0 Laboratory experiments

Friday November 19

09:00-10:30 Lecture on the use of microsensors to monitor water treatment processes (Akihiko Terada)

10:30-11:30 Course wrap up

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* Supported by: Technology and Natural Sciences doctoral Program *