Public defence in ecology: Dennis Amnebrink

Thesis title:

Seasonality influences gene expression in Baltic Sea microbial communities

Third-cycle subject area:



Faculty of Health and Life Sciences


Wednesday 5 June 2024 at 09:00

Place for thesis:

Room Azur, building Vita, Kalmar and via Zoom

External reviewer:

Dr Isabel Ferrera, Senior researcher, Spanish Institute of Oceanography, Malaga, Spain

Examining committee:

Professor Silke Langenheder, Uppsala University
Docent Dag Ahren, Lund University
Professor Johanna Witzell, Department of Forestry and Wood Technology, Linnaeus University


Docent Karin Holmfeldt, Department of Biology and Environmental Science, Linnaeus University


Professor Jarone Pinhassi, Department of Biology and Environmental Science, Linnaeus University

Assistant supervisor:

Dr. Daniel Lundin, Department of Biology and Environmental Science, Linnaeus University


Professor Anders Forsman, Department of Biology and Environmental Science, Linnaeus University


Wednesday 15 May 2024 at 15:00 at University Library, Kalmar

In order to receive the Zoom link for the thesis defense, please contact Faculty Administrator Linnéa Larsson: linnea.larsson@lnu.se


Prokaryotes are the most abundant living organisms in the marine environment. They contribute to primary production and the recycling of its products. Collectively they influence the marine element cycles of carbon along with elements like nitrogen and sulfur. However, much remains to learn of the functional characteristics of microbial communities carrying out these processes, and how different communities respond to changing environmental conditions in space and time.The composition of marine prokaryotic communities is known to change in a seasonal manner, but how seasonality influences their gene expression or “activity” remains largely unknown.

In this thesis I investigate the relationship between prokaryotic activity, relative gene expression, and seasonality using time series field data on gene expression combined with reference genomes of prokaryotic populations (metagenome assembled genomes, MAGs). This revealed pronounced seasonal succession in overall transcriptional dynamics. Importantly, roughly half of the 50 populations with highest relative abundance in transcription altered their transcriptional profiles across seasons. Thus, changes in relative gene expression on the annual scale is explained by community turnover and modulation of activity within populations. Characterization of a MAG representative of the filamentous cyanobacterial genus Aphanizomenon that forms summer blooms in the Baltic Proper, highlighted seasonal patterns in transcription of genes underlying key prokaryotic activities. This included genes related to photosynthesis (different genes expressed in different seasons), nitrogen-fixation (expression peaking in summer) and oxidative stress (peaking in winter). A mesocosm study in the Bothnian Sea using temperature and nutrient manipulations simulating the winter to summer transition showed lower growth efficiency and higher maintenance respiration in winter conditions, implying larger relative losses of CO2 through respiration in winter. Additionally, temperature, nutrients, and their combination, caused separation in both prokaryotic taxonomy and transcription of metabolic pathways. Key features included archaeal transcription of ammonium oxidation in winter conditions, and Oceanospirillales central metabolisms in summer.

Taken together, these results highlight the pronounced effect of seasonality on prokaryotic community gene expression and the capability of prokaryotic populations to alter their expressed genetic repertoire. This emphasizes the importance of the temporal perspective when considering how prokaryotic communities will respond to changes in environmental conditions.

Keywords: microbial ecology, time series, gene expression, metagenome assembled genomes, mesocosm experiment, Baltic Sea, pelagic, marine, seasonality, prokaryote