Applied and Environmental Microbiology

Applied and Environmental Microbiology

The focus of the Applied an Environmental Microbiology Group lies on one of the smallest inhabitants of marine ecosystems: the prokaryotic microbes. Microorganisms are found everywhere in the oceans but in coastal regions the interaction of humans and marine microbes is most intense. Research priorities of our group include the mechanistic analysis of algae-bacteria associations, microbiology of aquacultures and pathogenicity of bacteria. Since microbes may occur both as free-living cells or attached to particles, the formation and dynamics of particles in anthropogenic coastal regions as well as industrial applications are another hot topic of our group.

Algae-bacteria associations

Many coastal ecosystems often support enormous biological diversity, including structurally and functionally complex benthic communities, and provide key ecosystem processes. As a result, numerous delicate interactions may arise among species and their surrounding environments, making these ecosystems particularly susceptible to changes in environmental parameters. The presence of particular bacterial strains can be of significance for particle aggregation and therefore important in DOM-POM conversion. Aggregation of algae to the formation of marine snow is an important process in marine systems leading to the settling of POC predominantly in form of marine snow. In shallow coastal regions, sinking aggregates do not only determine the sedimentation rates of organic matter to the underlying sediments. Depending on current strength, they can act as vectors, transporting organic materials from A to B. As these materials may also include pathogenic bacteria, toxic chemicals or simply high amounts of organic matter, our group aims at understanding the role of aggregates as vectors in coastal ecosystems.

Microbiology of aquacultures

Because of the dramatic decline of natural fish stocks and the high demand for food security, aquacultures are becoming increasingly important. Ecological threats, such as eutrophication and biodiversity loss, as well as health concerns (e.g. the occurrence of pathogenic microorganisms) lead to current concerns about coastal aquaculture practices. Intense aquaculture practices may lead to anoxic conditions in the water column, the warm temperatures are ideal for the rapid growth of bacteria, including pathogens, and a high organic matter load (resulting from aquaculture wastes) provide an easily degradable food source supporting the proliferation of heterogenic bacteria.

Currently, projects based in Indonesia and Philippines investigate the abundance, diversity, community structure and function of prokaryotic microbes within and close to aquaculture impacted sites. Furthermore, screening for the occurrence of pathogenic bacteria in shrimp and fish aquacultures takes places, microsensor measurements of oxygen and hydrogen sulphide will be carried out and water quality parameters are monitored.

Pathogenic bacteria 

Gammaproteobacteria, including the Genus Vibrio, generally thrive well in warm waters with high amounts of organic matter load. Especially in tropical regions the occurrence of opportunistic Vibrio species derived from aquaculture impacted sites, not only harm cultures fish stocks but also are of risk to humans.

Therefore, together with monitoring environmental conditions of tropical coastal waters, we screen for potentially pathogenic microbes and presence/ absence of toxic genes using qPCR.