Linnaeus University Centre for Ecology and Evolution in Microbial model Systems

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.

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.

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.