Life can sometimes be found in places where it is least expected – for example in Arctic and Antarctic ice. Anique Stecher, a biologist at Konstanz University, is investigating the biodiversity in these areas using samples collected on board a research vessel and then analysing the data using special phylogenetic software. This provides her with a comprehensive inventory of Arctic and Antarctic organisms and with insights into their relationships with each other. The researcher’s findings make an important contribution to gaining an in-depth understanding of the studied ecosystems. She is also studying cold-adapted enzymes which have the potential to be used in foods and detergents, amongst other things.
“Although marine algae are essential constituents of polar ecosystems, biodiversity studies on the marine algal communities are still lacking,” Anique Stecher says. The researcher from Konstanz therefore decided to carry out the studies herself, and so she went on board the German research vessel 'Polarstern' to collect samples and is now using special software to establish DNA sequence databases. The research project is being carried out in cooperation with the Alfred Wegener Institute – Helmholtz Centre for Polar and Marine Research in Bremerhaven, Germany. Stecher did her master’s degree thesis at the University of Bremen and now works at the University of Konstanz where she continues to use the equipment of the Alfred Wegener Institute for her research.
She has already taken part in two expeditions to the Arctic and Antarctic during which she and her colleagues drilled ice cores from ice floes and on board the research vessel Polarstern sawed them into ten-centimetre-long pieces. These pieces were then melted using sodium chloride solution, whose high salt concentration protected the cells from osmotic shock and hence from changes in their transcriptome. The solution was subsequently filtered through a polycarbon filter in order to extract all the cells of a given ice piece community. The filters were shock frozen and kept at -80°C until they could be further analysed in Germany.
“The study of biodiversity is divided into two areas,” Ms. Stecher explains. “We do not want to just analyse the total biodiversity in the Arctic and Antarctic communities, we also want to find out which organisms and their genes of a given community are active.” The researchers are also interested in the phylogenetic relationship of the algae under investigation. Different methods are applied to address the different research issues: the researchers analyse certain parts of ribosomal DNA, i.e. DNA sequences that code for ribosomal RNA. However, these analyses also capture information on cysts and temporary stages that are not active (i.e. transcribed) in situ. In order to restrict information gleaned to the active proportion of the ice community, Anique Stecher and her colleagues are investigating parts of the organisms’ rRNA. rRNA is an essential constituent of ribosomes, assemblies of proteins and rRNA molecules that translate mRNA molecules to produce proteins. Since proteins are essential constituents of active cells, the analysis of rRNA provides important information about the active proportion of the Antarctic and Arctic algal communities.
The analysis of DNA and RNA sequencing data is associated with a big problem: “The sequencing of DNA and RNA leads to a huge amount of data, which can only be analysed with specific software,” said Ms. Stecher. Such software was initially unavailable and a large proportion of data had to be analysed manually, particularly the data for inferring the phylogenetic relationships between the individual species. The researchers from the Alfred Wegener Institute developed new software that enables the faster phylogenetic classification of DNA sequences. The PhyloAssigner is based on a reference database with known sequences which is compared to the new sequence data.
The database sequences are presented in form of a phylogenetic tree, into which the new data are also incorporated. “This is all done automatically, meaning we save a lot of time,” said the biologist. In addition to being used for Stecher’s data collection, PhyloAssigner can also be used for the determination of phylogenetic relationships of other organisms. The researchers will analyse the data with PhyloAssigner before going on to establish databases.
Anique Stecher will work on this project until October 2014. “Since our work is focused on basic research, it can bring about quite different results,” said Stecher highlighting that the work she is doing might make important contributions to obtaining a more detailed understanding of the Arctic and Antarctic ecosystems. In order to fully understand these ecosystems, researchers need to analyse biotic and abiotic elements in detail. These data can then serve as basis for predicting future changes, e.g. in connection with global warming.
Of particular relevance are enzymes of some marine algae. Ice structuring proteins (ISPs), also known as antifreeze proteins (AFPs), or ice nucleation proteins (INPs) are produced by Arctic and Antarctic plants, fungi and bacteria and enable them to survive in subzero environments. ISPs and INPs counteract the formation of ice crystals. There are numerous applications for antifreeze proteins; they are used to protect food against frost or to maintain the consistency of ice-cream to give just two examples. Enzymes of Arctic and Antarctic organisms are also of interest for the development of washing agents and detergents as they allow chemical processes to run at lower temperatures and therefore enable energy-efficient cleaning and washing.
“Most of the well-studied proteins originate from animals, mostly warm-blooded animals. They are active at moderate temperatures; human proteins work best at 37°C,” said Ms. Stecher. A temperature decrease of 10 degrees reduces the enzymes’ activity by 50%; they denature at temperatures of above 45 – 50°C and are hardly active at all at lower than normal temperatures. The situation is completely different for ice algae proteins, which work optimally at -5 to +5°C. “These proteins can help save energy. They have the potential to be used to wash things with cold instead of warm water and also run technical processes at lower temperatures,” said the researcher going on to add, “enzymes are not only chains of amino acids; they are folded into three-dimensional conformations, which gives them secondary and tertiary structures.” In addition, some enzymes only become active when several folded protein chains assemble into a multi-subunit complex (quaternary structure). Protein folding and the formation of multi-subunit complexes are the result of ionic and hydrogen bonds, which need to be more stable at higher temperatures. A protein that exerts its function in warmer environments needs to have a different structure than one that is active in subzero environments. “I am sure that these properties are of major interest for industry,” said Anique Stecher referring to her interest in working with a company.
University of Konstanz / Alfred Wegener Institute - Helmholtz Centre for Polar and Marine Research