Life without a mouth, stomach and intestines
Numerous plants and animals - including humans - are colonized by microorganisms that perform useful tasks for their hosts. Anyone who wants to take a closer look at their genome faces a problem: they usually cannot be cultivated individually. So four microbiologists from Bremen took care of it in one fell swoop.
Olavius algarvensis is a marine oligochaete living in the top twenty centimeters of sandy seabed in shallow coastal waters off the Mediterranean island of Elba. From an anatomical point of view, the worm is something special: not only has its digestive system been completely reduced – it has no mouth, stomach or intestines – it also has no kidney-like organs (nephridia).
While the reduction of the digestive system as an adaptation to symbiotic microorganisms is also known in other animals, gutless oligochaetes are the only known host group that have also reduced their excretory systems. For the worm, this means that all processes related to food intake and waste disposal must be taken care of by its symbionts.
Nicole Dubilier and her colleagues from the symbiosis group at the Max Planck Institute for Marine Microbiology in Bremen wanted to use this wonderful example of "outsourcing" energy production and waste disposal to find out how these essential host tasks could be outsourced to the symbionts. Investigating a symbiosis in detail is often a particular challenge, as most symbiotic microorganisms cannot be grown in isolation.
If you can't look at the details, you try the whole thing: the so-called metagenomic analysis makes it possible to isolate the individual genomes of different organisms without isolating the organisms themselves. But how can the mixture of genomes from the environmental sample be assigned to individual species?
In classical genome analysis, the genetic material of a specific species is sequenced using established methods, and every year scientists publish hundreds of different genomes in databases. However, the classic approach does not work for a mixture of different organisms because the assignment of the sequences is not clearly recognizable.
This problem can be illustrated with an example from text analysis: Imagine that the books of different authors are hopelessly mixed up. The texts are only available in fragments. The task now is to restore the original works. Since each author prefers a different style of writing, the original texts can be reconstructed using a statistical analysis of the fragments. However, in the genome "text" there are only the four different letters A, G, C and T. And these letters hang together without a "dot" and "comma".
Hanno Teeling from the Microbial Genomics group has now succeeded in solving this problem with a new mathematical algorithm, a binning method. The relative frequencies of all 64 possible groups of three of A, G, C and T, all 256 possible combinations of four of the building blocks and the frequency of G and C within a standardized genome segment differ significantly depending on the species of organism.
This allowed the fragments to be broken down into individual subgroups, so-called bins. The fragments could be assembled, read and the individual genomes reconstructed. Now the researchers had the key in their hands to reconstruct the respective metabolism of the symbionts and to show which metabolic pathways can be activated depending on the environmental influence.
The result: Two sulfur bacteria (gamma proteobacteria) and two sulfate reducers (delta proteobacteria) occur together in the worm. The Sulfate Reducers produce Reduced Sulfur Compounds, which the Sulfur Oxidizers can use as an energy source. This is how the symbionts feed each other in a syntrophic sulfur cycle.
Surprisingly, all four symbionts can fix carbon dioxide like plants - so the worm has become a veritable endosymbiotic powerhouse. All four symbionts are also involved in the decomposition of toxic metabolic end products such as urea and ammonium and thus contribute to the recycling of valuable nitrogen.
"The little worm shows how limited resources can be used efficiently through the interaction of coordinated microbial communities in the smallest of spaces," says Nicole Dubilier. Thus, the Olavius symbiosis could be a model for an almost self-sustaining biosphere. Comparable systems on a larger scale are being researched intensively, for example to be able to cope with longer interplanetary space travel such as the planned journey to Mars.© Max Planck Society
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