Research > Ongoing Projects > Functional Metagenomics
Functional Metagenomics to Study Prokaryotes from Arctic/Sub-Arctic Springs of Hydrothermal Origin
Department of Genetics in Ecology
Center for Geobiology, University of Bergen, Norway
Molecular biology and ecology of Archaea
Although prokaryotic in cell structure, Archaea have been recognized as a third primary evolutionary lineage, being as distinct from true Bacteria as they are from Eukaryotes. Phylogenetic and genomic analyses indicate that Archaea and Eucarya are probably sister groups that share a number of homologous factors involved in replication, transcription and translation. Therefore, the study of information processing in the simpler systems of the Archaea is often directly relevant for understanding cellular evolution and the more complex interactions that occur in the eucaryal nucleus.
Most cultivated archaea thrive under extreme environmental conditions, such as temperatures between 70 - 113 °C, low pH or high salt concentrations. However, with molecular ecological methods, specific lineages of archaea have also been detected in common place environments, as for example soils and the marine plankton. Their high abundance indicates, that these archaea should be of global ecological significance. However, their phenotypic and physiological properties are still largely unknown.
Our research interests involve
- the study of stress-induced transcriptional regulation in the hyperthermophilic archaeon Sulfolobus solfataricus and its virus SSV1 to get insights into global regulatory networks and into regulatory factors interacting with the basic (eucaryotic-like) transcription machinery in hyperthermophilic archaea
- the characterization of as yet uncultivated microorganisms, in particular of archaea, by metagenomic and novel postgenomic techniques
In order to study genomic and phenotypic features of uncultivated archaea and bacteria we have initiated an environmental genomic approach that involves the construction of complex habitat-gene-libraries and the isolation and sequence analysis of genomic fragments that are identified within these libraries. For this purpose we have developed and optimized methods for the isolation of high-molecular weight DNA directly from terrestrial and sediment samples (up to 600 kbp). We have constructed large BAC- or fosmid-libraries and have currently stored around 7.5 Gbp of environmental DNA from soils, sediments, bacterial mats, marine invertebrates and hot springs. These libraries have been used to characterize genome fragments of crenarchaeota (archaea) from soil and sponges as well as an abundant and little characterized group of bacteria, the acidobacteria. Furthermore, our environmental libraries serve as a rich source for the isolation of novel enzymes and drugs for biotechnological use.
The detection of genes for a potential ammonia monooxygenase (Amo) on an archaeal fosmid from soil led to the hypothesis, that crenarchaeota from soil might be ammonia oxidizers. We have shown in transcription studies on soil samples, that the amo genes are transcribed and induced upon addition of ammonia. The cultivation of a marine archaeal ammonia oxidizer and of highly similar amo genes from marine environments in other laboratories recently supported our hypothesis of a widespread occurrence of ammonia oxidizing archaea. Using the amoA gene, encoding the A subunit of the key enzyme ammonia monooxygenase, we have now shown in qPCR studies that ammonia oxidizing archaea in both pristine and agricultural soils outnumber ammonia oxidizing bacteria by one to three orders of magnitude, not only in top soils but in particular also in greater depths.
Current and future investigations involve
- the quantification of ammonia-oxidizing archaea under various environmental conditions and attempts to cultivate representatives from various habitats for more detailed physiological and biochemical studies.
- the monitoring of the nitrification activity of archaea in environmental samples. For this study, we investigate the reaction of archaea to various inhibitors, such that we can distinguish both groups (ammonia oxidizing bacteria and archaea) in natural samples.
- A novel ongoing project has been initiated on hot springs in Iceland.