Cyanobacteria and eukaryotic algae live in rapidly changing environments and often have to adapt to changes in light availability in the minutes to hour time scale, significantly shorter than their generation times. How do these phototrophs acclimate to these conditions? How is photosynthesis regulated and how do they protect themselves against the damaging influence of a surplus of light energy as caused by high irradiances or by nutrient limitation? We study these acclimation patterns by measuring photosynthetic activity with a suite of different techniques, but also investigate the regulation of the expression of the genes involved in photosynthesis and photoprotection. By studying different species we try to understand the differences in photo-adaptation and -acclimation by different groups of phototrophic microorganisms. Measurements are carried out in the field as well under controlled laboratory conditions in cultures. A practical application of the research is the development of time series of phytoplankton primary production, using automated variable fluorescence technique to measure photosynthetic activity.

Natural phytoplankton populations are often limited in their growth rate by nutrients. Because of the decrease of nutrient loads many formerly eutrophic systems actually go through a period of “oligotrophy”. Understanding the limiting factors for the different phytoplankton populations is a prerequisite for understanding ecosystem biodiversity and function, but measuring the limiting nutrient is difficult. Often the used proxies (nutrient concentration and – ratios) do not give information on the actual limiting nutrient. For this reason, we will study by using cultures the regulation of genes involved in the uptake of nutrients and we will develop new methods based on molecular biology to detect nutrient limitation in natural phytoplankton populations. The focus will initially be on genes involved in P-uptake because management measures aiming at the decrease of P-loads have been more successful than those aiming at the decrease in N-loads.

Only prokaryotes are capable of utilizing the omnipresent atmospheric N2 as a source of nitrogen. Nitrogenase, the enzyme responsible for N2 fixation is extremely sensitive to O2 and is also energy demanding. The oxygenic phototrophic cyanobacteria have evolved a variety of adaptations to fulfill the requirements for N2 fixation. We study these adaptations and investigate how they are dictated by the environmental conditions. We study N2-fixing cyanobacteria in pelagic open ocean settings and in estuaries and coastal seas as well as in benthic microbial mats. The key players are isolated in pure culture and their properties studied in the laboratory. We use a combination of measurements of N2 fixation by the acetylene reduction assay and stabile isotope techniques and molecular genetic approaches for instance by measuring and quantification of functional gene expression and fluorescence in situ hybridization. Eventually we will attempt to find molecular markers that allow the identification of N2-fixing cyanobacteria in present and past ecosystems.

Phototrophic picoplankton is the dominant primary producer in aquatic ecosystems. This group of organisms is highly divers and it is clear that many different types are coexisting together or are adapted to specific niches. Many picoplankton species have specific adaptations with respect to the nutrients (e.g. nitrogen) they can utilize, or to light intensity. Moreover, many species have adapted to the efficient use of only part of the underwater light spectrum by producing a variety of typical pigments. We study the diversity of phototrophic picoplankton in isolated pure cultures at the genetic level, analyze their characteristics and attempt to identify their niches in the natural environment using a variety of techniques, including flow cytometry and fluorescence in situ hybridization.

Coastal microbial mats consist of consortia of micro-organisms that form a complex vertical stratified ecosystem. They are primarily driven by phototrophic microbial communities and maintain a nearly closed cycle of biochemical elements. Due to their relative simple composition, confined dimensions and their role in biochemical cycling and ecosystem functioning, microbial mats form important model systems for studying ecosystem function and the development of ecological theory. It allows us to study basic processes of microbial evolution, genetic exchange and interactions between the different species occupying a microbial mat. Currently, coastal microbial mats are of specific interest because of their role in beach-sand stabilization and initiation of dune formation. With our current awareness of the predicted dramatic effects of climate change, global warming and rise in seawater level these microbial mats may play an important role in coast line defense. Despite intensive physiological, ecological and taxonomic studies, hardly anything is known about the mat’s genetic makeup, diversity in metabolic traits and interactions between key players. To unravel both the genetic potential and the actual proteins expressed in a microbial mat, two state-of-the-art techniques will be combined into a novel research line. Through a combined genomic and proteomic approach, the complex interactions between different micro-organisms can be studied. This approach allows us to get insight in the genetic potential of a microbial mat and in the actual expression of genes and proteins in response to environmental variables and diurnal changes. In addition, this approach may lead to the discovery of novel genes encoding bioactive compounds (e.g. antibiotics, or specific enzymes) that may be of biotechnological or medical interest.

The ability of bacteria to rapidly adapt to changing environmental conditions is well established. However, the evolutionary and genetic mechanisms underlying molecular adaptations and the sources of genomic diversity are poorly understood. Candidate processes for both are the acquisition of external genes via horizontal gene transfer and changes of the primary sequences of protein-coding genes. In addition, genomic rearrangements due to the activity of mobile elements are a frequent source of diversity of microbial populations. Contrary to the majority of bacterial genes, the diversity of mobile genes is, however, most likely shaped by the reproductive interests of the selfish elements. In order to determine the relative contribution of these mechanisms to microbial diversity, we study these three aspects of the genomic diversity of publicly available cyanobacterial genomes. Collectively, these studies give a comprehensive overview of the dynamics of genes and genome regions in cyanobacterial genomes. These studies will also provide insight into adaptation and co-evolutionary processes at disregarded levels of microbial diversity. We collected evidence for molecular adaptation in a number of cyanobacterial genes involved in photosynthesis, nitrogen fixation, genes of selfish elements, host defense, and circadian rhythms. The accumulation of genomic data now makes it possible to formulate hypotheses of molecular adaptation of larger genome regions. To this end, we will combine data from metagenomics and complete genomes.

Marine sediments play an important role in the mineralization of organic matter. Organic matter processing is mainly done by the highly diverse microbial community. However, it has been proven difficult to relate processes and community structure, mainly because many of the detected microbes have no or only a distant affiliation with cultures. Accordingly, their role in biogeochemical processes and interactions with other members of the community remains unknown. We address this gap in our basic knowledge on structure-function relationships in microbial communities by using techniques that combine stable isotope labeling to track processes and biomarker labeling to identify active, functional groups of microorganisms. One focus is on the development of an rRNA magnetic-bead capture protocol that will allow us to target specific phylogenetic groups of sulfate-reducing bacteria. We also study how functional groups of bacteria are related to general environmental characteristics such as carbon mineralization rates.

We study chemoautotrophic bacteria because they are important for the re-oxidation of reduced compounds such as sulfide and ammonium that is produced in anaerobic sediments. Re-oxidation is an important process in coastal sediments and on average explains 70% of the oxygen flux. We are studying chemoautrophy by labeling sediments with 13C-bicarbonate in the dark and tracking the label into lipid biomarkers such as PLFA and archaeal ether lipids. This allows us to study rates and distribution of chemoautotrophy in relation to sediment redox zones, and also to identify active microbial groups. We also plan to further identify active chemoautotrophic bacteria by studying the diversity of functional key genes involved in the various chemoautotrophic pathways as found in prokaryotes.

The oldest fossil stromatolites date back 3.5 billion years and represent the oldest remnants of life on Earth. Stromatolites are laminated rocks that were formed through lithification (silicification, calcification and/or diagenesis) of benthic microbial communities. Microbial mats are often considered as analogues to fossil stromatolites. Although the majority of modern microbial mats do not lithify, there are a few examples of living stromatolites. We study the physiology and ecology of modern microbial mats and stromatolites, investigate how they survive periods of burial and the conditions under which calcification takes place and stromatolites are eventually formed. The results are compared with examples from the paleontology record.

The department of Marine Microbiology maintains a unique collection of (marine) cyanobacteria and microalgae. Currently the Culture Collection Yerseke (CCY) comprises ~500 strains: ~300 cyanobacteria, ~150 diatoms, and ~50 other eukaryotic algae, most of which are available as pure (axenic) cultures. In this project we improve the methods, media, and culture conditions for the isolation and cultivation of phototrophic microorganisms, identify the isolated strains pheno- and genotypically and develop protocols for their long-time (cryo)preservation.