Linnaeus University Centre for Ecology and Evolution in Microbial model Systems

The research that is carried out at the Linnaeus University Centre for Ecology and Evolution in Microbial model Systems (EEMiS) is focused on marine environments in the Baltic Sea – on the border between sea and land, in coastal waters and in the open sea.

Our research

The Baltic Sea is a vulnerable environment which is strongly affected by human activities in the surrounding countries.With research expertise covering the entire Baltic Sea food chain from the smallest microorganisms to fish and birds, the Linnaeus University's largest research centre, EEMiS, forms a cutting-edge in the research for a healthier sea.

Even if the researchers focus on a specific aquatic system, it is basically not very different from other aquatic ecosystems. The processes behind the interaction between organisms and the large-scale consequences they may have on an ecosystem's function are roughly the same. By studying the Baltic Sea, the researchers will also be able to contribute with results and knowledge of global significance.

Research for a healthier sea

The Baltic Sea is a vulnerable environment which is strongly affected by human activities in the surrounding countries. The Swedish government has also designated the Baltic Sea as an ecosystem of special societal significance. 

We live in an ever-changing world and all organisms, including human beings, are affected when the habitat changes. Some changes in the environment are natural and predictable, such as seasonal variations in weather conditions.

However, ecosystems are also affected by human activity in the form of eutrophication caused by over-fertilization, overfishing, or the emission of greenhouse gases which contributes to global warming. The effect of human actions becomes more acute as a result of the population growth and increasing urbanisation. This may have serious ramifications for – among other things – biological diversity and the distribution of organisms and genetic variation. In turn, this will eventually have negative consequences for the health of both people and animals as well as for food production.

In order to understand the effects of these environmental impacts, we need more knowledge about the very smallest organisms. Microorganisms interact with all living creatures, from microscopic algae to humans. For example, phytoplankton is important for the stock of animals and plants in our seas as they produce carbon and nitrogen which are indispensable for marine ecosystems. But certain types of phytoplankton, such as cyanobacteria, also produce toxins which – in combination with eutrophication – can harm marine life and eventually humans.

Microbial model Systems

By concentrating their efforts and using microbial systems in their research work, the researchers at EEMiS will be able to exploit an almost vacant niche in the research community and contribute with important new insights.

Traditionally, evolutionary ecology research has focused on the larger, conspicuous animals and plants with spectacular shapes, colours, habits and behaviour.

In our research we study microorganisms, which are very suitable for experimental research, even if they at first may appear rather inconspicuous. Their smallness, rapid growth and short generation time means that both complicated and slow processes can be studied in a small space and a short time. Despite this, they have rarely been used when trying to solve general ecological and evolutionary questions.

Furthermore, ecology, evolutionary ecology and microbial ecology are by tradition regarded as different disciplines, which has previously made multidisciplinary research much more difficult.

Internationally prominent research

The fact that the centre has attracted funding from a wide range of sources, which support the different EEMiS projects, is proof that this is an important matter for society. Support has come from the European Commission, the European Science Foundation, the Swedish Research Council (Vetenskapsrådet), the Swedish Research Council Formas and others.

The experience and expertise of the seven researchers involved in EEMiS is in great demand and they are often invited to review research projects in other countries, which shows that they are successful and well-established in both national and international scientific arenas.


Research groups

At Linnaeus University Centre for Ecology and Evolution in Microbial Model Systems (EEMiS) seven research groups investigates how microorganisms interact with each other and with other organisms in their environment.


Time and Place: 13.00 in A137 (if not otherwise stated)

1-2 February

EEMiS Workshop

21 February

Room B221

March 7

Marielle van Toor (postdoc) and Josanne Verhagen (postdoc), group Jonas Waldenström, EEMiS, Linnaeus University.
Title: "Unraveling how viruses keep traveling: waterbird migration and avian influenza virus evolution"

21 March

Karen Labret, Postdoc, LnuC-EEMiS.
Title: " From population genetics to community analyses: my journey towards the understanding of plankton ecology"

4 April

Emil Fridolfsson, LnuC-EEMiS. Half time seminar.
Title: " Transfer of vitamins and pigments in the aquatic food web" (Room KSL332)
Room KSL332

11 April

Mohamed L. Merroun, Associate professor, Department of Microbiology, University of Granada, Spain.
Title: "Microbes and metals: environmental perspectives and industrial benefits"

18 April


2 May


16 May


30 May

Domenico Simone, LnuC-EEMiS.
Room KSL332

13 June

Room KSL332


Within the center we have a wide and unique basis to overview the entire Baltic Sea food chain. The six different research groups are working on their own specific projects, and interact at the same time in joint projects within their different specialties. Three of the joint projects are:

Ecology and evolution of marine anoxic sediments

In this project we are studying how microorganisms use nutrients in the sediments in anoxic environments of the Baltic Sea. By understanding the microbial processes in anoxic sediments, we can find strategies to restore the dead areas of the Baltic Sea.

Oxygen concentrations in marine sediments may increase or decrease due to natural seasonal variations during the year, but anthropogenic activities such as nutrient loading can accelerate oxygen depletion and eventually void the sediments of all oxygen. If undisturbed by turbulence, such as in the deep sea, the sediment may be permanently anoxic. We are interested in how the microbial populations and their functions cope with such changes, and how we can relate molecular biology data to chemical fluctuations affected by changes in the oxygen level. These data have the potential to aid the design of strategies to remediate anoxic zones.

Sediments are environments that host a vast amount of organisms, ranging from the small (microbes) to the large (bottom dwelling fish). Many organisms larger than microorganisms depend on oxygen for survival, while microbes are able to utilize other electron acceptors than oxygen for survival. Hence, in anoxic sediments microbial life may still thrive by respiring e.g. nitrate (denitrification) or ferric iron (iron reduction). Due to nitrate yielding more energy as an electron acceptor than ferric iron, profiles of chemical substances can often be seen in the sediment depth. Microbial processes such as these and other chemical redox processes cause sediments to be complicated systems. Even though life seems to be difficult in anoxic sediment (sometimes also called "dead" sediments), life actually still exists in the prokaryotic domain.

We are studying the microbial composition and their functions in the surficial zone of marine sediments. We are interested in how changes in the oxygen level, nutrient states, presence of cyanobacteria and abiotic stresses affect the population composition and gene dynamics. Measurements are conducted on many of the chemicals that can be used by microbes for survival. The molecular biology data and the chemical measurements are then compared to give answers on e.g. microbial ecology and adaption rates. One method to study sediments is to use a gravity corer, and then to incubate the sediment cores in different conditions and measure chemical fluxes over time. We then use modern molecular tools such as 16S sequencing, metagenomics and metatranscriptomics to learn more about the microbial life in the sediments and how they change over time while oxygen levels either increase or decrease.

Ecology and evolution of defensin genes in Mallards

The perpetual struggle between hosts and their pathogens has intrigued scientists for decades. Invading pathogens can cause disease, and even death, in their hosts. As such, there is strong selection on hosts to develop effective protection against these pathogens. The immune system is the principle mechanism for protection against pathogens in vertebrate animals, and is essential in combating infection and disease.

This project aims to understand how genetic variation in immune genes is correlated with susceptibility to disease in Mallard ducks. Specifically, we are interested in defensin genes, which encode small peptides (50-100 amino acids) Duckthat form an important component of the innate immune system of vertebrates. As such, they are integral in allowing individuals to mount a rapid response to a wide-variety of invading pathogens, such as bacteria, viruses and fungi.

We are characterising defensin genes in Mallards with known infection histories, with a view to understanding whether certain defensin genes or alleles afford individuals with higher resistance to disease. Mallards are an important reservoir for avian influenza and other wildlife diseases. Avian influenza is a viral disease of birds, and has received global Andfällaattention over the last decade when it was discovered that certain subtypes, such as the highly pathogenic H5N1, could jump species barriers and cause severe disease, or even death, in humans. Mallards have long been recognised as the primary wildlife reservoir of avian influenza viruses, and the disease can spread rapidly from infected to uninfected individuals, including other species.

During autumn migration, Mallards from distinct populations aggregate at stopover points, including our study site at Ottenby Bird Observatory on the island of Öland. And i handThis results in individuals coming into contact with disease causing pathogens, including avian influenza, they may never have encountered before. As such, innate immunity is likely an extremely important mechanism of disease resistance in this system. By investigating how diversity in defensin genes correlates with individual propensity to contract diseases, we aim to understand how infectious diseases shape the ecology and evolution of the host species which they infect.

Ecology and evolution of fish microbiology and immunity

Animals constantly encounter and interact with a wide variety of microorganisms, some are pathogenic, but many are harmless or even beneficial. In this project we are interested in exploring and understanding the structure and dynamics of microbial communities in wild fish populations. Microbial interactions with their hosts and the environment are one of the driving forces of the evolution of both microorganisms and the animals that the microorganisms interact with.

Fish of the same species may inhabit very different habitats, ranging from marine to fresh water settings. The different environments may not only have different microbial faunas, but also differ in abiotic factors, such as pH, salinity and Fisk1temperature. While some fish tend to live their whole life locally, some individuals migrate. We are investigating the impact of the microbial composition on fish.

Specialized cells on the surface of the fish produce large glycoproteins that in contact with water swell and make up the slimy mucus experienced by anyone who has tried to get hold of a slippery fish. This mucus layer, which is in direct contact with the surrounding water, has many important functions (including innate immune defence) in the fish. We are currently investigating the microbial community residing in the mucus of various fish species.

It is well known that the intestinal microbiota is vital for us in shaping our immune system. Since this symbiosis probably originated when vertebrate life still only was found in sea, this is an intriguing area to investigate in an evolutionary perspective. Thus, we are also interested in the intestinal microbiota of fish.

Many different molecules involved in the innate immune system and protection against pathogens can be found in the mucus. Hence, we are also interested in antimicrobial components of the fish mucus. We are currently trying to characterize the genetic diversity of small antimicrobial peptides, defensins, of the three spined stickleback.