Metagenomics

Imagine a pile of beautiful books in front of you. Now imagine they have been cut into small snippets, each containing individual words and sentence fragments. You are now given the task of bringing order to this chaos. The best way to start would be to search for keywords. If the snippet says "Hamlet", it probably belongs to Shakespeare’s work of the same name. And if "new speak" or "Big Brother" comes up, you’re probably dealing with George Orwell’s 1984. "Muggles" and "Hogwarts" would clearly point to the Harry Potter series. In this way, you can dig through the pile of paper, piece by piece, and try to sort and reassemble the snippets. If several copies of the same book have been cut up differently, this makes things a bit easier. Overlapping text fragments will give you additional clues as to the correct composition of the texts.

Metagenomics isn’t all that different. Instead of books, researchers work with the genomes of micro-organisms that they cut up and reassemble. The snippets are fragments of the genome or "sequence segments". Computers can help to assemble the individual parts. There are now excellent algorithms for dealing with such a task. Some sequence segments are also already known and stored in databases. These can help to assign certain sequences to groups of organisms or functions.

With the help of metagenomics, it is possible to analyse an environmental sample (i.e. a mixture of the most diverse organisms as they live together in the environment) and find out which organisms live in this environment as well as which genes – and thus metabolic pathways, interactions, and defence strategies – predominate. This distinguishes meta-genomics from classical microbiological methods, which specifically search for individual organisms (groups) for which the genome sequences are known. Bioinformatics refers to the methods used to bring order to the metagenomic analyses and data.

Metagenomic methods also allow us to identify microorganisms – regardless of whether they can be cultured in the laboratory – and thus to study the dynamics in populations over days and even years. We can thus gain insight into the complexity and change of the communities our microscopic co-inhabitants. However, metagenomics often cannot stand alone; without classical microbiology, we would be unable to interpret the results.

The molecular ecology of algal blooms

For example, we use meta-genomics to study the degradation of algal blooms in the North Sea: every year in spring, when the days get longer and the sunlight increases, many phytoplankton species multiply rapidly – and their population grows exponentially. These algal blooms are of global importance for the carbon cycle. During photosynthesis, the small algae convert carbon dioxide into sugar compounds and oxygen. Within a few weeks, the algae run out of nutrients, and predators spread. The algae bloom then collapses. The bacteria then multiply en masse. They decompose the remaining algal biomass, and the bound carbon is largely released in the process. However, these processes are still not well understood. Which marine bacteria grow when? How do they process the algal biomass and release the carbon? What processes are behind this?