Lichtgedanken 03

S C HW E R P U N K T 38 and materials are transported from the soil through the underlying rock strata. »The microbiomes in the forest soil and groundwater are usually totally diffe- rent worlds,« notes Prof. Küsel. These microorganisms are significantly diffe- rent in the way they live. The profes- sor for Aquatic Geomicrobiology adds: »Therefore, when we find soil-dwelling organisms in groundwater, it is no coin- cidence.« She cites the fact that surface organisms enter the groundwater as evi- dence for the close connection between habitats above and below ground. Although most Archaea from the soil do not survive long in water, the resear- chers have found evidence of Archaea in groundwater samples over the entire transect. According to them, this shows that the microorganisms must enter the groundwater along the whole transect. »Above all in the Hainich area, where the groundwater aquifers are relatively close to the surface, there were large numbers of the microorganisms in the water,« says Küsel. The organisms that are most likely to survive their move from the soil into the groundwater were identified as »Thaumaarchaeota« (from the Ancient Greek »thauma«, meaning »miracle«) and »Woesearchaeota«, na- med after the US microbiologist Carl Richard Woese. Scientists today mainly use the methodology of genome sequence analysis to identify microorganisms in soil or water samples. Compared with earlier me- thods, such as culturing microbes on growth media, this has the advantage that one can also analyse organisms which it has not been possible to culture to date. In addition, the high-throughput technique provides results very quickly and is much less labour-intensive. A »genetic fingerprint« of the microbes is used for identification. As with an ac- tual fingerprint, it can be compared with the other samples and in this way, orga- nisms that are already known can be clearly identified. However, this technique additionally enables researchers to identify previously completely unknown species and determine their relationships. In the first step of the procedure, the DNA is extracted from the microorganisms found in the water or rock samples. Great care must be taken in doing this, to avoid contamination with other microorganisms present everywhere in our envi- ronment. The DNA fragments thus obtained – usually very few in number – are subsequently copied in large numbers using the »Polymerase Chain Reaction (PCR)« method. The genetic information is then »read out«, which means that the DNA is sequenced. Among other things, what is known as 16S rRNA is of interest in identifying microorganisms. This denotes segments of ribosomal RNA (rRNA) that are pre- sent in all organisms and are preserved throughout evolution. The ribosomes are complex structures made of nucleic acids and proteins, which occur in all cells and on which protein biosynthesis takes place—a universal process of life. The 16S rRNA gene is highly conserved, which means that it is present in all organisms, but it is also characterised by very high variability. In publicly ac- cessible databases, there are now thousands of sequences of 16S rRNA genes available as reference sequences, which enable immediate identification. This method is not only used for analysing environmental samples. It is current- ly applied virtually everywhere that microorganisms need to be identified, for example for detecting pathogens in clinical diagnostics. Knowledge of 16S rRNA provides not only the basis for detecting a specific microorganism in a sample. As this ribosomal RNA has barely changed in the course of evolution, it is also a kind of »molecular clock« . It enables researchers to classify each species in the universal tree of life and identify the most closely related species. With the aid of the ribosomal RNA gene sequences, the currently generally ac- cepted phylogenetic tree has also been created. This divides the organisms living on Earth into three domains: Bacteria, Archaea and Eukarya—to which all the higher organisms such as plants, animals and fungi belong, among others. As far as microorganisms are concerned, it is currently estimated that only one to five per cent of all species are known to date. For more than 90 per cent of all Bacteria and Archaea, we only know their rRNA sequences, without ever having cultured them in a petri dish or having made them visible under a microscope. B A C K G R O U N D Photo above: drilling core from a Schillkalk bench (Upper Muschelkalk). The fissures widened by karsti- fication represent groundwater flow paths. Photo right: sampling groundwater in the »Hainich Critical Zone Exploratory« at a location used as pastureland. F E AT U R E