Genomic signatures of anthropogenic stress on revived diatoms from natural archives


The Foundation for Baltic and East European Studies

Project type


In recent times, anthropogenic activities like agricultural and industrial processes have raised temperatures, CO2 levels and nutrients at a global scale. Oceans are at a great risk of contamination due to the dumping of industrial and human waste and climate change. Oceans are also major sinks for heat and CO2 and will consequently warm, acidify, and deoxygenate in the near future. All these will have adverse effects on biodiversity and food webs and lead to global warming.

While short-term ecological effects have been characterized for many anthropogenic stressors, we essentially know nothing about long-term evolutionary effects and the underlying mechanisms affecting marine biodiversity. How can we predict the impact of anthropogenic stresses on the health of marine biodiversity over a long timescale? One attractive way is to look back and study how past human-induced stresses may have already affected marine biodiversity.

The central idea is that the past is the key to the future!

It is noteworthy that microscopic marine phytoplanktons account for ~50% of global primary production. Resurrection ecologists have long recognized deposited sediments as sources of viable seed or egg banks which can be used to look into the past. Human-induced eutrophication and climate change have increased pollution and hypoxic zones in the Baltic Sea leading to drastic changes in marine biodiversity and the ecosystem. Hypoxia is recorded during three ages in the open Baltic Sea: ~8000-4000 calendar year BP (Holocene Thermal Maximum, HTM), 2000-800 cal. yr. BP (medieval era), and 1800 AD till date (modern era). High diatom resting spore abundance is found during these ages: HTM, Medieval Climate Anomaly (~1000-700 cal. yr. BP), and the last century. Hence, diatoms from Baltic Sea sediments from these time periods will be an ideal model system to study the impact of humans over millennia for the following reasons:

  • Diatoms constitute one of the most diverse and ecologically important groups of phytoplankton.
  • They produce viable propagules that are incorporated in the sediment record.
  • The Baltic Sea is one of the most contaminated seas, and therefore, the diatoms must have experienced anthropogenic stresses over long time scales.
  • The marine diatom Chaetoceros, one of the most abundant and diverse genera worldwide, is found throughout the Baltic Sea stratigraphy from the Littorina Sea about 8000 cal. yr. BP till date.

This project will disentangle how human- and climate-driven processes serve as drivers for adaptive responses and evolutionary changes over thousands of years in the marine diatom Chaetoceros in the Baltic Sea. In this project our aim is to reconstruct ~7000 years of diatom evolution in relation to changes of their environment. It will also help to predict the ecological and evolutionary trajectories of marine biodiversity in the Baltic Sea.

The four main aims of the project are:

  1. To measure and compare the genetic variation in diatoms from recent and ancient sediment revived resting spores as indicators of evolutionary changes Chaetoceros muelleri resting spores from three time periods, including both i.e. recent (present) and ancient (~1000 and ~7000 cal yr BP) will be revived. First, the reference genome and a de novo transcriptome of C. muelleri will be generated. Second, genetic differences between the sediment revived recent and ancient populations will be identified.
  2. To measure expression levels of genes indicative of evolutionary change and stress response Transcriptomes will be obtained from the populations from the three time periods to examine the gene expression levels and also validate the genetic markers identified in Aim 1.
  3. To assess fitness changes in populations from three ages The changes in fitness of the populations from the three ages will be measured by recording changes in growth rate, cell density, chl a under high and low salinity and light intensities.
  4. To identify links between phenotype and genotype Single nucleotide polymorphisms will be identified from populations in Aim 3 to infer links between genotype and phenotype. Transcriptomes will also be generated from populations in Aim 3 for comparing gene expression levels and confirming phenotypic and genotypic links.

In this project we will assess two main research questions:

  1. What is the proportion of the genomic change that can be attributed to environmental changes caused by human activities inducing selection? (Aim 1)
  2. Which genes (or gene complexes) are correlated to the phenotypic response characteristic for changes in environmental conditions? (Aims 2-4).


New undisturbed sediment cores from the Baltic Sea will be collected since fresh sediment is essential to a successful outcome of resurrection of resting spores. A sampling site in the deeper part of the north western Baltic Sea proper will be located using sub-bottom profiling. Stratigraphies which contain preferably laminated sediments with high diatom preservation will be cored using a combination of long piston and short gravity core sampling. Methods Resting spores from the three ages will be revived and grown in cultures. DNA will be extracted, amplified and sequenced. Population genomic studies will be done to estimate the differences in the genetic architecture between the three time periods. The genes underlying the phenotypic responses of growth rate, cell density, chl a concentration to changes in light and salinity conditions will be estimated.

Anushree Sanyal: researcher at the Department of Forest Mycology and Plant Pathology; Division of Forest Pathology, Swedish University of Agricultural Sciences

Elinor Andrén: Associate Professor at Södertörn University

Thomas Andrén: Associate Professor at Södertörn University

Stefan Bertilsson: Professor at Swedish University of Agricultural Sciences

Conny Sjöqvist: Postdoctoral researcher at Åbo Akademi University, Finland

Research area / geographic area

Natural Sciences, Technology and Environmental Studies Biology Geography Environmental Science Environmental Studies Nature & the environment Baltic

Project time

2020 — 2023


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